There are ways to avoid that without nerfing abilities you don't like. If everyone is based on say, 250 points, you're going to get people designing 150 point attacks because they won't have points left over enough to be effective.
Assuming everything is fitting to concept, as long as everyone is based on the same number of points, they will, more or less be balanced. That's the foundation of the Hero system, that 50 points spent in one place is equivalent to 50 points spent on somethign else. The GM has control of the world they live in, but if you take the only control the players have (character creation), then you might as well play something else. The GM has control over the environment and over the NPCs. Play to the character's disads, whether that means kidnapping their DNPCs, or forcing them into a situation where the powers they bought aren't effective (maybe they have to solve a puzzle instead of killing the bad guy).
The main problem is you're trying to balance something that's already balanced. Sure, it can be abused, and abuse should be stopped, but trying to make new rules to keep abuse from being possible limit everyone else. Cars can be abused, but we don't just take all the cars away from everyone, we just punish abuse of it. I say until a character abuses a power (or designs a power specifically for abuse, like 1 gazillion nonrecoverable charges, etc.) let them use it, with the knowledge that abuse will be punished.
If a character with FW uses it too much on one character, and splatters him with one hit, people will notice. Cops will arrest the character because he used way too much force, the villains cohorts will all gang-rape the character, etc. Be creative. Creative answers that stop things are better than the non-creative "GM says no."
The point it to have fun. Have fun with it.