They are useless...as skills. The bonuses they gave are useful and can/are repurposed in the game in other ways.
That is solving the problem. To get speed perks you have to lose perks somewhere else. It's not like as you level up everyone gets the same perks. Perks diversify characters even more than they did in the past because it's an entirely different aspect of stat changes. Also, if you say that "Well everyone is going to pick the speed perks so we are still just as fast" well the same goes for stats, everyone is just going to pick athletics and Acrobatics and everyone will have the same speed. I for one will not be picking speed perks because I don't need speed when everyone falls before me as a pile of ash.
Yes, but unless they have heavily revamped running speeds versus alternate methods of transportation, I
can see everyone picking up the speed perk. Fast characters should be able to move roughly 50% faster than the slow ones while running. Can you seriously say that you wouldn't run 50% faster all the time at the cost of only one perk? Especially when we're getting 50 of them, a single perk would be trivial compared with the bonuses increased speed would grant.
If they are making perks have many levels, I could see this issue being balanced. If each rank only gave 10% and could be taken 5 times, I can see how taking that would be a serious sacrifice when they could be taking many other perks instead.