Looking at the racial weapon abilities, and many of the class abilities that read: +1 attack, or +1 damage, or +1 attack and +1 damage with X weapon, or under Y condition, all with multiple ranks, I can't help but feel that these are incredibly boring wastes of space.
Yes, we all want more DPS, but ultimately the game gets kind of balanced against the numbers we have, so inflating our DPS and to-hit will only, eventually, result in a reciprocal increase in monster HP and AC. I like being able to specialize in a weapon, but spending 8 AP to do it? That's pretty dull, and for most weapons, it still doesn't elevate them past the strongest choices we have without specialization anyway (khopesh, scimitar, rapier, bastard sword, falchion, Epic Sword of Shadows).
I like the dwarven enhancement that ends up adding Con to damage with certain weapons, as this is unique, influences build decision, and has a much larger impact on your weapon selection. Even a +4 attack bonus, with the way the altered to-hit system works, is often irrelevant, or nearly so.
I'd prefer to see more abilities that really make using a particular weapon unique, or unique in your hands, and competitive with the big-ticket weapons. In the leaked enhancements preview of the rogue, we were looking at rogues who were turning their daggers and kukris into low-damage-die khopeshes. I'd like to see more of that for the feat-starved classes. I'd like to see more abilities that allow us to use a non-standard stat for attack and/or damage. I'd also like to see some more original abilities included as part of our specializing: bonuses to certain tactical feats with the selected weapon, additional on-hit, crit or vorpal effects, debuffs, added defensive abilities, etc...
Compare the longsword and the bastard sword after the addition of glancing blows. Using the latter is more interesting than the former, even though they are otherwise almost identical, because the latter encourages different build decisions and a slightly different playstyle (occasionally). I would like to see more differentiation between weapon like that, and weapon specialization enhancements are a good place to do it.