Though Players start the game as under powered villains, they shouldn't end the game that way. Estimating the number of sessions in your Semester, give your players enough XP after each session so they can earn the powers of -almost- an adult villain by the end of the game. This doesn't mean they can defeat Super High... the Villains' foes will grow in power along side them, maybe even faster, and certainly with a greater focus on violence.
As your players earn XP, give them the opportunity to grow their powers, and buy off some of teh limitations they started with. Weak attacks can grow in power, Painful mind-control can become more bearable, or completely new powers can develop as the Villain progresses through puberty.
Assets acquired easily in-game should be short lived, lasting no more than 1 or 2 game sessions. This is to reflect the danger of their mission, and give a clear benefit to persons who paid for their assets at character generation. For example, a crappy, unreliable car purchased at character gen will be consistently available to players, and is less likely to be watched by police than a stolen car. That stolen car should get stolen again, chased by police, or wrecked within a single game session.
Assets acquired through role-play should be rare, and can be added to a player’s permanent assets. For example, Peter Peterson, an NPC security guard that was fired as a result of the players’ facility break-in may (through roleplay) get rehired as a henchman, as long as he has reason to trust his new employer. These assets should be paid for between games with an appropriate amount of saved experience points, but the important part is they can't just be bought, they have to be earned.