I personally think Thief has three main problems:
1) SE dramatically overestimates the frequency with which you can land SA and TA in an 80% Haste environment with even only 3 DDs, and they also dramatically overestimate the benefit of landing SA and TA. When I look at the WSs and gear they give Thief, I become more and more sure that they're assuming almost every WS THF does is stacked with SA or TA. Realistically, Thief seems to use these JAs about half as often as they theoretically could because situations that encourage one tend to discourage the other. Also, THF with Haste gear and magic Haste TPs dramatically faster than SA and TA timers can support, even assuming capped merits and no positioning problems.
TAing in Dynamis, easy! Plenty of people hitting the monster so one is bound to stay in front of you.
SAing in Dynamis, hard. The monster is spinning.
TAing when lowmanning with a second DD, easy! Just run behind him and WS!
SAing when lowmanning with a second DD, hard! It's a minute into the fight,t so you both capped Enmity already and the monster is just spinning.
Look at Torcleaver (4.5 fTP, 60% VIT) and Tachi: Fudo (3.65 fTP, 60% STR) and compare them to Rudra's (3.25 fTP, 60% DEX). Those are non-crit Empyrean WSs for 2H weapons with more than twice the base damage of Twashtar. Torcleaver's mod is a laugh, but its fTP and base damage wreck us. If Dagger got a comparable non-crit WS, it would not be a shade under 6 fTP to compensate for the base damage. The problem, of course, is that Thieves (and Dancers) can already get lucky and pull off 5-6k Rudra's when our Crit-forcing JAs work. If they essentially doubled the fTP to make it useful when it's not stacked, we'd be doing 10-12k Rudra's when we get lucky using our crit-forcing JAs.
Now compare it to Blade: Hi (4 fTP, 60% AGI, crits). This is what makes me think they're assuming THF holds TP for SA or TA to be up. In order for Rudra's to be better than a 0-crit Hi, it has to be stacked or nearing 200 TP. Then again, they could just not be thinking at all. I mean, look at Camlann's Torment. Still much better damage than unstacked Rudra's, but it would make me pity Dragoon if they didn't have access to Drakesbane.
2) The enmity system is actually a big part of Thief's DD problem, because I feel SE wants to avoid giving them the ability to instantly cap someone's VE and CE in one WS (~6600 damage). If they gave Dagger a comparable WS to Tachi: Fudo, THF could easily do thousands of damage on anything from the front and give all the enmity to someone who was just hate-reset. I think SE wants to avoid making their hate-moving JAs too powerful, not that it matters in the current state of play.
Enmity fix would be easy. Either increase the cap by a factor of 5 or decrease the enmity of all actions by a factor of 5. Then further halve the enmity generated by doing damage. No one has to struggle to keep hate off the mages right now even if they're spamming Cure 4, because we do so much more damage than we cure HP. Make it harder to hold hate through damage, problem solved.
3) The final problem for Thief at the moment is just the state of the game. Abyssea has eliminated HNMs that are 20 levels above us. Mercy Stroke, for instance, used to be mediocre to good in merit parties. It really shined on HNMs though, because forcing a crit on something with a lot of Defense or a much higher level than you is much more important than doing so on a trash merit monster. SE is possibly trying to avoid giving the only job that can evade really high level monsters the best tools to damage them. I think this is likely also why Thief doesn't have native Subtle Blow, to make them a less viable tank for high level stuff.