1) I can understand complaining about free abilities tying your character to fluff you do not want, but not when the free ability is so small as being automatically trained in Thievery. A +5 bonus to one skill is not a character straitjacket.
2) You can't auto detect rogues by looking for people with daggers. Do your Fighter characters not carry backup daggers? When they're walking around in a city out of armor so they can shop, do they not have daggers with them? For that matter, don't your Wizards carry backup daggers? I thought everyone carried a backup dagger. I thought this was standard issue adventurer gear. Sure, the Fighter's special attacks might not work with a dagger. But so what? First, it makes sense that a dagger and a greatsword require different training. But more importantly, from a gamist perspective, that fighter has a big attack bonus, a good strength score, and a pile of hit points. If he's stuck using just a dagger for roleplaying reasons, he should be just fine.
3) A Rogue with a dagger is not objectively better than a rogue using another weapon, even though Rogues get +1 attack roll with a dagger. This seems pretty clearly designed to improve the viability of the dagger so that it isn't automatically overshadowed by the shortsword. Right now, in 3e, a dagger isn't a great choice as a primary weapon because the Rogue can already use the larger, more damaging shortsword. The Rogue Weapon rule provides some equality here, making the shortsword more damaging but the dagger more accurate.
4) Finally, as an overall point, it is likely that a great deal of variety will be provided by the class powers selections. You can't leave these out of your consideration, as they're the way you customize a class. Arguing that the rogue is too restrictive while not considering all the different tactical options provided by power choices is like arguing that the 3e Fighter is too restrictive while ignoring the existence of feats. Of COURSE its restrictive, if you leave out the greatest source of variety.