If they balance it right, where should be the problem?
Indeed, we don't even have any clue what the perks do, or how powerful they are, or how many they are, judging whether or not the amount of perks available in the game will unbalance it based on Fallout is rather foolish. Now, it certainly is very possible that Skyrim will have balance issues, and it is not impossible that some of them will come from the perks in the game, but it's too early to assume this will be the case. Besides, there's some speculation that perks will play the role of attributes as well now, and you could always increase your attributes every level in past Elder Scrolls games.
Honestly, though, I was never bothered by the amount of perks available in Fallout 3, it only really became a problem when they raised the level cap to thirty in a game never meant to go beyond 20, in my opinion, not that Fallout 3 didn't have its balance problems, but they didn't come from the amount of perks available, I'm not even sure I approved of reducing it to one perk per two levels in New Vegas, for one thing, it meant that gaining an odd number of levels felt really unsatisfying because rather than feeling a sense of accomplishment that I had gained another level and become stronger, I just found myself hoping I'd get to the next level soon so I could choose a new perk. Moreover, while in theory, granting players less perks as a whole meant that the choice of perks carried more weight, in practice, what it really did was made the worthless perks, which the game still had a number of, even more worthless. "Here and Now" was already a horrible perk to choose in Fallout 3, in New Vegas, it's even worse because not only do you waste one chance to choose a perk, of which there were only 15 instead of 20, but you don't even get to choose a perk on the level you gained from choosing said perk.