GM Fiat has the same role on their side of the table that Hero points have for players. If you feel like it's cheating, then switch back to the hard constraint of a set number of villains points for you to spend. PCs get HP when you fiat, so it's not they have much to complain about for the occasional use.
And really, forgot about system specific stuff. If you have 5 guys teamed up against 1 guy, and each person is roughly equivalent, then things are usually going to be an easy win for the 5 guys. 5 10th level guys in DnD versus 1 10th level fighter and some low level flunkies will be over even more quickly.
If you want challenging foes without too high a PL, you need to stack the deck a bit. Create a situation that favors the foe. Remember that PL isn't really correlated to power points, so the foe could have lots of tasty extras on his powers. Area and Aura are especially good when someone who is going to be outnumbered, since one can affect every PC and the other works when people attack him - making the PCs' extra number of actions into something of mixed blessing. Impervious can help too, but it can also be really frustrating for certain players. Pick on weak saves.
Or use villain team ups.