The Thief, while one of the stronger overall professions, alongside the Guardian and Mesmer, has its own issues, just like any other profession.
To sum things up, its central issues are low weapon variety, extreme weapon inequality, poor underwater skills selection, and certain bad traits and utilities.
Dagger / Dagger
Fine. No downsides. Synergizes reasonably.
Dagger / Pistol
Fix the rooting bug on the Dual Skill and it will be fine.
Fine. No signfiicant issues.
Pistol / Dagger
A condition damage set that lacks in cover conditions - too easy to remove. Dancing Dagger was overnerfed. Body Shot is just bad. Overall, however, this is a fun and mostly-synergetic set.
Pistol / Pistol
An awful set that displays poor synergy all around. 1 and 3 do not synergize. Body Shot is awful. Black Powder doesn't particularly synergize with a ranged weapon. Head Shot does poor damage for its cost. No way to enter stealth. No escape. Main damage source is a mediocre, high-initiative, easily-avoided move. Set is boring to use in general.
Sword / Pistol
With the Pistol Whip nerfs, the Thief is generally better off auto-attack, but this is otherwise a solid set. Infiltrator's Strike could use some work n terms of bugs and clunkiness.
Sword / Dagger
Weak Dual Skill. Needs a faster animation and higher damage or a faster animation with a lower cost. Dancing Dagger was overnerfed.
Get rid of Body Shot in favor of a short backwards leap that allows Pistol / x Thieves to combo finish with Black Powder and better kite enemies. Add on a weak burning or poison for a cover-condition or rework Vulnerability as a condition to effect condition damage - both Vulnerability and Condition Damage builds could use some buffing.
Increase initiative cost of Nine-Tailed Strike (Spear 3). It's currently a free, spammable block - which speaks of poor design.
Thieves are currently stuck with only their weakest elite (Basilisk Venom) and a poor selection of utilities underwater. Most of their Tricks, all of their Traps,and their Deceptions can't be used underwater. That's about two-thirds of their slot skills! That is a serious issue and makes underwater a frustrating experience at best for them.
Rework their underwater utilities to give them some variety. They are already missing valuable dfensive moves like Black Powder - don't rub salt in the wound.
Improve trait support for:
Make Last Refuge a Major. A Minor trait that can get you killed is bad design.
FIX FLEET SHADOW.
Improve non-Ambush Traps.
Fix bugs with Smoke Screen that can cause projectiles to ignore it.
A melee weapon used with the Acrobatics line to block, counter-attack, and leap around.
Improves condition damage builds by providing access to Burning. Used to distract foes, stealthing allies who are a sufficient distance away from the thrown Torch. (Like a reverse Shadow Refuge).
Mace (Both Hands)
Provides the Thief with disables. You are a sapper now.
Provides the Thief with a block + counter and a ranged, single-target nuke. Dual Skill stealths with Sword / Sword.
Stationary camouflage coupled with slow, high damage attacks. 1200 range.