CG's are good, and if you have enough stats like CG, W, K, etc, then people would be stupid not to have starters pitching. I don't usually do H2H, but I don't recall having IP minimums.
I think you're trying to control how people manage their teams too much. Don't make it so everybody should have 3 starters with a 4th who spot starts in favourable matchups. Make some rules which are fair for everybody, and if they want to punt W, CG, and K for a better chance at ERA and WHIP, then let them.
I like the idea of using % categories like SB% and K/9 or K/BB as well. It would make efficient players like closers and stud setup men very valuable, and marginal starters probably wouldn't be selected at all. So you could do:
BA, OBP, SLG, SB%, RC/9 and W/L%, K/9, ERA, WHIP, SV%
That would be interesting and different than most leagues. Bad baseball players would lose their value, since you'd be judging by quality not quantity. An IP minimum would be neccesary if it's H2H or else you could just ahve a couple relievers who get a win and a save, with low or zero ERA/WHIP.
Personally, I like the conventional 5x5 or 6x6 with BB and Holds. But you said your league likes the different settings, so combining the two types isn't a bad idea.
Most of that post was thinking out loud, but hopefully some of it was helpful