I say Roto. I think it is unfair for a team to get like 10 losses because one or two of their pitchers have a bad outing in a week, just like it is unfair for a team to have a ridculous amount of HR's, and have it all be for naught since the other team had 1 more. I actually think Roto is just as fun as H2H, and it makes bragging rights easier to use, since the best team wins basically every time.
If your playing with friends you meet often or know well, do yourself a favor and stay with H2H. I use to be a Roto-only guy for a long time but recently I've play in a couple of H2H leagues (baseball and basketball) with some old high school buddies and I can tell you, the fact that its one on one makes the entire league so much more livelier. Since your all seniors, you might even consider a keeper league. When your all off to college next year, the league will keep your old buddies together.
I don't see this pro-H2H argument mentioned, so I'll go ahead and mention it: Head-to-Head tries to mirror the two-sided competition of real baseball. It feels like active competition, rather than the gradual amassing of statistics.
Real baseball isn't just about who has the "best team," but who has the best team on any given day, and it is affected by a laundry list of external factors (weather, day-to-day injuries, slumps, attitudes, call-ups and send-downs) that influence team victory and defeat on purpose or by accident.
Do you activate a Vlad Guerrero listed as day-to-day for the upcoming scoring period? Such a dilemma involves enough risk to engage the player-for-fun and enough Cost-Benefit Analysis to statistfy the most strategy- and number-enamored player.
In our league, we play a little bit of both. There is a roto champion and a H2H champion in one league. It keeps guys playing until teh end instead of being stuck at the end of the roto.
In four years, the roto winner has won H2H only once. We have the playoffs and the hot team usually wins the H2H playoffs. Still, the money gets spread around and we have fun.
Our league is predominantly guys from the same area that played ball together. It is our way to stay in touch and gab baseball. We throw in $40 a piece and the cash gets moved around a lot. The worse is to finish last in H2H. That cost you a 24! Second last cost you a 12.
Expos... Gone, but not forgotten.
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Based on what you said, I might suggest tinkering a bit with the categories to add some additional strategy on the H2H side. Perhaps you just need to add a bit of something new to it to keep it interesting.