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.