I've recently been exposed to M&M for the first time and was quite impressed by the versatility and customisability. An important knock-on effect of this customisability which shouldn't be overlooked is the mental shift in the charcter creation process: the GM's input is required when assigning effects and points values to Complications, when applying non-standard Extras to a powers or when deciding which powers should be allowed to share an Array. Little things help reinforce the authority of GM interpretation over the "it's in the book so I can do it" approach that plagues many D&D DMs.
So hopefully your player's shouldn't go mad with munchkinning when you give them the carte blanche of the points-buy system.
Just in case they do, watch out for anything involving the Transform power, Variable Power Structures and large Arrays:- Transform and Variable PS both explicitly state that GMs should monitor them carefully to make sure it's under their control; Jerthanis has already said a thing or two about Arrays;

Quote Originally Posted by Jerthanis View Post
For another, some powers, like Cosmic Energy Control or Magic allow you to buy almost any power for a steep discount with (so far as I can tell) no disadvantage.
The disadvantage of Arrays is, if you fill it with sustained/continuous abilities then you can only have one active at a time. If it has nothing but attack abilities (or similar instantaneous effects) then you wouldn't be using two at the same time anyway and so gain versatility for a nominal cost. And remember there has to be some sort of thematic link!