I think TRON's capacity is also lower than Splash Mountain's. The TRON hourly capacity may be slightly higher (I'm not sure about that), but Splash Mountain is 8 minutes long; TRON is about 60 seconds. That makes a big difference.
I also think Splash has a larger customer base than TRON -- Splash does have the big drop, but the ride is nowhere near as intense overall as a roller coaster, and TRON's seating is apparently an issue as well? I'm just speculating, but I'd be very surprised if there weren't a higher percentage of MK guests interested in riding Splash Mountain on any given day than will be interested in riding TRON.
Of course that latter concern doesn't matter as much if the rides are full all day every day anyways.