Assassins are indeed about getting behind a target as quickly as possible, and delivering as many backstabs as possible. Daggers do not do much good with frontal attacks, to the point where if you miss a backstab and the enemy turns around, it's better to end your turn and save the AP than to keep attacking.
However, my warning about lowering the base 3 AP cost of 1H weapons isn't about dagger damage, it's about the damage of non-dagger 1H weapons. If 1H weapons cost 2 AP, that means they can do a lot more attacks than they can now, which would make them overpowered because they ARE meant for frontal attacks and so they have much higher damage.
One other reason why I'm not so sure about the "let's think of 5 levels of bonuses" for all weapon specs is because before this patch, Daggers normally cost 2 AP and could backstab, and those were taken out to put into Way of the Rogue, seemingly to find something to put in there. I'm not sure they could think of 5 levels of bonuses for 1H, 2H, Bow, Crossbow, and each bonus would have to be tested and balanced, and the game is supposed to release in less than two months.
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I agree that it can be hard to balance different weapons. One of the reasons why I suggested lower crossbow range is because they have the same range and skills as bows, with greatly increased damage and an extra 2 AP cost.
The idea of lowering the effective range was to have different niche's for the two weapons - the crossbow does more damage, but requires you to put yourself at greater risk by needing to get closer to hit targets more effectively.
There is normally a simple rule for something like that: if people always take A over B you should just erase B from the equation. Either you make skills valuable or they don't have a right to exist.

I'll just say this:
Right now, I'm not likely to ever put points into "Weapon Specialization" instead of "Way of the...". Weapon spec adds 10% damage a level, which will add up to 50% extra damage eventually, but inevitably, it's going to be secondary to getting the next tier of spells or skills. I'm not sure there's a fix for it, because a new tier of skills is basically always going to be more interesting.