The first question is what site? Yahoo, ESPN, and other places have different available settings. I think that ESPN has more available, but I like both. As far as settings, the standard 5x5 tends to work best for roto, although it makes H2H a lot less stressful. I like both ratios and counting stats to be present. In my keeper league, we have a 8x8. Is that too much? No because that's what we wanted. You could go with a 6x6 as well. The problem that you are facing in your league is basically called streaming or flooding. In roto, you can't do streaming as succesfully. However, in H2H, the man with more K's, W's, QS, and SV's normally wins. Here's the stats that I suggest.
If ESPN, then
Hitting: H, R, HR, RBI, SB, AVG, OBP, SLG - these are solid and don't really require too much thinking. Compared to a 5x5, a guy like Adam Dunn is worth more because he only hurts you in AVG and helps you in OBP AND SLG, just an example. I like hits too because it can help give more value to lead off hitters who don't have the best AVG as well.
Pitching: W (or Losses), K, CG, SV, ERA, WHIP, BAA, QS - CG can be hit or miss, but you'll be surprise how many your guys get on a week to week basis. I like having 3 ratio categories because it helps balance against the streamers. If you don't like BAA then you can always use something like K/9, which adds value to RP. Or you could have OBPA, which to me is too much like WHIP.
I like having an 8x8 because it really makes it fun to micro manage your team every week. Is it time crunching? Absolutely, but aren't all fantasy sports like that?! I hope that this helps. Oh, if you choose Yahoo! then BAA is not available, so you can use K/9 instead.