You will most likely get many different responses to this one.
I like 5x5 categories in H2H leagues, (specifically R,RBI,SB, OBP, SLG, W, SV, K ERA WHIP) -- of course you already have a set of categories for your league, so you'll probably want to stick with that.
The positions and such really depend on the provided you'd be using. I like basic positions: (C, 1B, 2B, SS, 3B 3OF UTIL). If your league has not too many managers (<15) it makes sense to throw in a CI,MI and one each of OF and UTIL.
I don't like having two catchers, although in a weekly transaction league it makes more sense than in daily.
I'd also see about not only having starters and a bench, but also a minor league roster, with a limited number of moves to the main roster. whether this makes sense for your league or not greatly depends on how involved everyone is...
the number of slots really ought to depend on the number of managers in your league.
You clearly need an innings minimum for each week. Barring that I don't think you need or should have specific RP or SP slots. if someone only wants to start starters -- let them... if someone just wants to start relievers, that's fine too. the former will win the countables (except saves) the latter has a shot at ERA and WHIP... don't fix the strategy for everyone in the league -- let them choose.
Give a man a fish and he'll eat for a day, teach a man to fish and he'll drown because you forgot to teach him to swim.
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