Well, the only disadvantage I can think of is that if you don't use it your LEDwiz is useless
That's not entirely true, PowerMAME also has 'GPWiz49 Auto DRS', which is not related to the LED-Wiz at all. This and the 'Pause Message' feature are the only extra features that aren't LED-Wiz specific at the moment, though more features are planned.
Horseboy, if you mean does PowerMAME have any disadvantages vs regular 'vanilla' MAME, no. If you wanted to, you could completely dis-regard PowerMAME's extra features and use it just as you would regular MAME.