This is the first inFamous game I copped, but let's say half way through (which I am currently) you unlock all powers on one side, then you completely go rogue and choose to go the opposite way, can't you still unlock the other powers? I'm assuming you can, and if so, then it's not like you are not able to get everything you want it will just take longer. Which is what I believe you mentioned above. But as a developer, why wouldn't that be a good thing. People who want to be able to have everything has to play the game longer.
I don't know. I really don't see an issue. If you want everything it'll take longer to get. If you don't then you don't have to worry. Either way you have choices..... which is what the game is intending you do.