if you are independant of the alliance you can count on not being able to get needed supplies from the games only source.

also access to basic game objects can be denied by a system that can be player controlled.

allowing your enjoyment to be denied by other players.

I've played EVE online, and even under the most agressive blobs there is still a chance, slim as it may be, to get any object in the game because the NPC's cant be turned hostile to you by players.
 

Well, yes.

The game's greatest asset is also it's greatest weakness.
It is actually cool that you can virtually anything as a player in that game..
On the other hand it is (at the least) frustrating that the needed game mechanics are not in place to support you.

That leaves you in a peculiar spot at times, such as being able to form up your own empire but not having the tools.to operate it independently from other, existing empires.
The game mechanics also foster some... problematic dependencies, such as a civilian relying on the military for protection from the "open PvP" and certain individuals then using that dependency to justify some kind of claim over you, just because they are part of that military.
Picture a common soldier raping a civilian and getting away with it, and even thinking he's right because he's got the "power" to do so.

That is it's greatest weakness:
That this game relies heavily on the players themselves to provide both fun and needed support and, above all, the creation of an enjoyable environment where it is FUN to play.

Since everyone has their own idea of "fun", but only some have the will and means to impress that view on others, a very FEW players are enough to deprive others of their fun.

But contrary to what you say, it is not a matter of allegiance (faction you are in):
People that use whatever "power" they have against fellow players are found EVERYWHERE (yes, in EVERY faction in THAT game and in every game).

If you want to do your own thing, but still HAVE TO (which is the case unfortunately) use another faction's facilities, then the GAME (it's mechanics) simply force you to create an ALT to get what you need and carry it where you can transfer it to the char that actually needs the stuff.

I have to disagree to some extend. Leaving the Alliance does mean that you as a faction become independent from it. which means then that you do not have any right to use Alliance facilities or get Alliance protection. That is why you are independent and it is one of the reasons why there have been requirements implemented that have to be met PRIOR one is able to declare or request independence.  

Basically there is nothing wrong with being independent at all! I do know that for a fact as I am playing a Civ within an independent faction. All you have to do is set up your colony and make sure it is able to self-maintain itself. Everything one needs to be independent, such as defenses, bases, outposts and even buildings, such as a cloning center, med center, shopping mall, etc. can be obtained and built on a colony.  

All you have to do is getting a colony and set it up right BEFORE you declare your independence. Get everything done you need. Built the buildings you need, get defenses, etc and you wont have any problem with the independence at all. If you do still need something from an Alliance core world, there is nothing wrong with that as well. Just use diplomatic channels to request a visa or travel permit or even take on diplomatic negotiations.  

It is all possible if one would really want it... however, being independent is difficult - very difficult, if not because of the reason stated above then because of the fact that there is no one who will defend you. If the other races go after you as they wish there will be no one to defend you other than your own ships and your own facilities. It is a quite big task and it takes a lot of time, money and effort it however can be done... 

In my personal opinion the biggest issue with being independent is the fact that you need a lot of manpower for it. You need crew for your ships who patrol your space, who do mining and cargo runs for you, etc. Especially if you want to work out a real structure within your faction, it will be quite manpower consuming. Winning players for your thing is however not that easy, especially with the limited player base available. 

@BenjiB:
You have missed the OP's point entirely.

Yes one can become independent (with one simple click actually).
Yes you CAN prepare your colony before you do that.

HOWEVER:
Once you ARE independent, you won't have access to NEW stuff added to the game, unless
a) you somehow manage to stay "on good terms" with certain people or
b) you use an ALT to buy what you need, incognito.

This is simply because the needed MECHANICS are not in place.
You cannot buy a spaceport, for example, or an equivalent of Geneva (where you get colonial charters) or Nelson's
(the shop on Terra that sells schematics and ships and colonial buildings and where for example bounty hunter licences are issued).
You cannot hire NPCs and set them up to sell these things.
So, all your preparation is only good for as long as nothing which falls in one of the above categories is added.

"Just use diplomatic channels"...
That is besides the point, because the OP has specifically said that the very PLAYERS that are "responsible" to issue them might just be the very same ones that (mis)use that power.
So basically, you are forced, by the lack of game mechanics, to "metagame" and use an ALT to get what you need.
There is simply no way to TRULY become independent as of yet.
And looking at the implementation speed and (lack of) development focus, there probably never will be.

"you need a lot of manpower"...
Is true and at the same time not as much:
To set up and operate an independent colony you need no(!) additional help.
Even with just an Atlas for a ship, it was possible to supply a distant colony - a task made that much easier with the addition of the Titan.
Mining is a joke now in this game, a task made meaningless by the Dev's ever since they have upped the yield by a factor of 30 to 50 (3 to 5 more yield per asteroid times 10 times the yield per refining).
Defending "your space"... yes that would, optimally, require additional manpower (to effectively crew a PvP ship).
However, since in this game SECRECY is your greatest asset, you are best off when noone knows about your "independent" colony and without the security opening that comes with recruiting what turns 90% of the time out to be an ALT of some other established (metagaming) player.
Besides, if your colony location is known (and you perhaps want to take part in the "political" game in/of SQO), then any amount of manpower might not help you because:
Certain players have been known to use (or at least want to) NPC ships to attack a colony.
For example, the then-admiral of the Alliance wanted to send the NPC fleet out to crush the newly-formed "ICS" back then, even wanted to be empowered to do so in every similar case.
Some people will simply use whatever "power" they have (and that CAN be significant) to "keep players in line" - THEIR line of thought of course.
It was this kind of players (not many but a few can be more than enough) that the OP's post was about.

What would be needed to TRULY become independent is the ability for a colony to install their "own" NPCs that sell the same stuff that is sold on core worlds.

I am aware of the fact that with a simple click you can technically declare independence. However Alliance Constitution and law states differently. If one would declare independence before the requirements as stated in the constitution are met and without passing a vote for independence in the parliament you would not be recognized as independent nation nor would you be allowed to act as one. 

The reality with this has been that those trying anyways would be 'visited' by the Alliance fleet to take care of the issue quickly besides that you would get really nowhere because of the lack of recognition. This rule does however make some sense too as if you become independent you should be truly independent. Having a colony with no real defenses and just 2 people on it will be barely recognized as an independent nation. I do have to agree though that certain circumstances in mind it would make sense to move away from this practice. 

This said I do have to agree that it is still difficult in some cases to be independent for said reason. However, even full independence can be achieved if someone is really after it. We do not want to forget here, that Confederation of Non Aligned Worlds is exactly such a faction. It is difficult and not that easy but it can be done. 

Alliance constitution is invalid, really.
a) It is admin-imposed and player-ran
b) It only applies to alliance "citizens".
The only "justification" for bringing the alliance law onto the table is that alliance colonial charters are unfortunately the ONLY ones readily available: which is another design flaw.

What sense does it make to play "with the rules" (and to stay within the limits of alliance law, you'd have to do so for about 3months), when all you want is to get away from them?
That "RP" crap about alliance colonies being alliance citizens and that it would justify sending the fleet ships (which are, btw, more powerful than what ANY independent faction could ever field as the closest ship is the ARES and that is merely a beefed-up Icarus)...
If that were true, then why do we see so many abandoned, and completely forgotten and unadministered colonies?
No fleet there to mop up, nor to inspect - much less to PROTECT.
No fleet inspecting the far-out colonies neither regularly nor irregularly.
They (all colonies, but especially those outside "colored" space) have to fend for themselves, from the start.
And by that logic, they are entitled to be independent from the start as well.

However, the MAJOR flaw is, as i said above, that as an independent faction you simply do not have the in-game tools to TRULY be independent.
You cannot build a military-grade ship, not even with in-game research or something.
You cannot install the above-mentioned NPCs that sell all the new stuff (like colonial buildings) as they are added to the game.
You cannot install NPCs that sell ships or give those core-world cargo missions needed to be truly independent.
(and you cannot do so even AFTER your colony is large enough to produce every possible product - instead you have to rely on the old colony-colony missions generated by your OCS)

The ConW is a faction of incative forum players - if they had three active players (that play exclusively in that faction), then it'd be a lot.
And the ConW also has had their share of unwarranted (NPC) fleet visits.
Recently there one or two factions that underwent the "lawful" proicess to exactly prevent the "RP" reason for the alliance to interfere with the military.
But with proper game mechanics, this would not be needed.

From a pure setting up and administering point of view, it is very EASY to set up an independent colony/faction and keep it supplied, with the above-mentioned exception to being able to acquire newly added stuff and military hardware.
But because of the missing mechanics, one has to wonder if it's "worth" it.
And after all, this thread is ALL ABOUT those missing mechanics, and not about political consequences etc.

edit: sorry about the missing format, the page's editor kind of lost it from the type/edit to the display