A guy named Simpson made a nice Excel character builder for M&M. You can find the latest version at the following address:
http://www.elyzium.net/mnm/
Also, you might want to check out the forums at
www.mutantsandmasterminds.com - the people there are very friendly and helpful.
Finally, talking of possible problems, there are a few powers you might want to watch out for. Incorporeality for one can become problematic with it's 'only one type of attack can injure me'. Sorcery and especially Cosmic Power, while valid and expensive powers, can make a character the Swiss Army Knife of superheroics - able to do practically everything that the rest of the group can do and somewhat overshadowing the proceedings.
Using the 2:1 skill rule is a good idea too. Oh, and just to mention a slight rules alteration from D&D and the like which you may or may not be aware of, in M&M Power Attack can be used with ranged attacks.
You may want to consider using an optional rule regarding Super-Speed and Super-Dexterity.
1) SS and SD both provide a bonus to your Defense equal to their power rank.
2) When two people who both possess SS/SD fight, subtract their Power Rank in SS/SD from the Defense bonus their opponent gains from SS/SD or, if their rank in SS or SD is higher that that of their opponent, cancel it altogether. This only applies for attacks the two people with SS/SD make against each other.
This lets super-fast and agile people fight each other on a more even footing, rather than having the vaguely ludicrous spectacle of two super-speedsters/uber-ninjas constantly failing to hit one another due to their high Defense values, despite their speeds/reaction times being comparable and hence not really capable of providing them with any advantage against the other.
Hope that's useful!
Synch.
