My Space Fantasy game is loosely based off of Farscape, which is a "non-supers" game, but we have people who heal others with mystical abilities, float in the air, and paralize others with 8 foot long tongues.
And in pulp we have the "Shadow," the "Phantom" as well as scientists who either don't know which end of the gun to hold or can shoot a fly out of the sky while inventing the atomic bomb 20 years early. The key to this idea train of thought is that even though these guys don't leap buildings in a single bound, they do have abilites that bend the laws of reality, as we know it now 80 years later.
1.) Mutants and Masterminds has a rp element to each power that player has, called the "Power Source." It is the label you put on a power to designate how the character got the power. You can have two characters who both have two levels of Super Dex, but one labeled his power source "Mutation" to show he's naturally quick, why the other character labeled his power source "Training" to show that he spent years honing his reflexes to get there. The idea lets players come up with human characters who are on par with other characters without making them "inhuman."
2.) For my game though, I do put a limit on attributes beyond human norm. For MnM, that limit to 2 levels of super attribute. I also started the game with the PCs at a PL of 5 instead of 10.
3.) You should go down the list of MnM's super powers and decide what powers you should prohibit or limit to make the game feel right for you. Flight and Incorpreal are the two tops on my list. Now that doesn't mean that if a player comes up with a good concept, such as the Rocketeer or Ghost Girl, I will say no. But I will keep my eye such characters to make sure they don't get out of hand. Or if I think the player's motivation is to get an unjust advantage compared to the rest of the group, I'll nix the idea.
4.) One thing you have to watch for is a player's temptation to buy a new power just because it is "neat." I have had one player who wanted to create a psionicist, now his powers are all over the map with level 1 this or level 2 that.
5.) On the other hand, it's been really easy to design funky stuff that would have been a pain through standard d20. As an example in my game, I haven't seen any rules for cybernetics in d20 that I really liked. In MnM, they are just window dressing and I can go on. The game does add a little more work to lower powered NPC, but then it makes high powered NPCs and funky powers much easier to work with.
