Run it as the rules are written and when you encounter a situation where you believe you have a better idea or game mechanic then give it a try.
Game Judges have been doing it this way since the game came out nearly 24 years ago.
Just last night I was reading through some of the Marvelphile articles. In one of them, the writer wrote that he has a house rule that when characters are "under fire" he permits them to make Dodge FEATs, even though they may have already used their alloted actions for the round. However, instead of the character getting the full -2, -4, or -6, he halves it to -1, -2, and -3.
He then wrote that if you like that idea, feel free to use it.
What I liked about what he wrote was that he is a fella who was a "official" contributor to TSR and actually Game Judged MSH. Even the brainiacs who helped the game along during it's 8 year run used their own house rules.
Heck, I wouldn't be surprised if Jeff Grubb even came up with rules that he used but never had published.
Bottom Line: You can make your game as simple or as complex as you like. The rules are extremely flexible.
If you come up with some house rules, you are welcome to share them with the Forum.
Regardless if we at the Forum like what you may come up with, what matters is this: Does it work for you and is your group having fun?