This isn't the same situation and it's pretty weak on your part to compare a two hander to a one hander that swings about 3 times faster.
How so? Two-handed weapons have disadvantages for using them over One-handed weapons in the same fashion that Crossbows have over Bows, it is very much comparable. The only reason Crossbows don't have their own skill tree is because the devs don't want to change the max level, and adding a skill tree for one weapon type would be going back to what Oblivion's skills were, which I highly doubt the devs want.
A crossbow is quite comparable to a Two-Handed weapon being that it's much heavier in it's use. It does more damage, similar to two-handed weapons, and it's slower in the sense that after you shoot it, you're left wide open for attacks while performing a slow reload animation. It even staggers often, similar to two-handed weapons.
A bow is quite comparable to a One-Handed weapon being that it's much lighter in it's use. It does less damage, similar to one-handed weapons, and it's quicker in the sense that you can knock an arrow much faster than a crossbow reloads, you can choose WHEN to knock your arrow, and you can even launch said arrow prematurely for some quicker damage to get that last sliver of health.
How can you not justify higher crossbow damage for the disadvantages that it has? I'd really love to know what exactly you guys want crossbows to be....lower damage than bows? What would be the point of using them, then, if they're lower damage than bows AND slower than them, honestly?