regarding protests, they should be like the replay flag in NFL. two strikes (original ruling upheld, ie coach protesting was wrong), and no more for the weekend. and a small fee (only if original ruling upheld) also keeps them honest, say $50 (think $100 is excessive, I never carry that much cash , DW wont let me)
I do like the idea of refunding the fee if the protest changes the ruling. If the umpires were correct then the fee applies for holding up the game, if the umpires were wrong the team is not punished for insuring the proper call. Sounds reasonable to me.