I'll repost something that a mechanical engineer and experienced AA repairman (who has done substantial maintenance work at both Disney and Universal) said on the matter.
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He singles out all-electric figures in this case as opposed to traditional hydraulic and pneumatic designs because the electronics don't play as well with extremely damp environments.
Splash/TBA is also more of an extreme case of this than other boat rides. There's a large number of drops kicking up a ton of water into the air throughout the entire ride. POTC by comparison only has drops in the starting cavern areas, and AA's are kept pretty far away from these drops in areas where the flume is less turbulent and less moisture is being kicked up into the air and onto sets. Splash/TBA's drops are not only much closer to many AA' heavy scenes, but the figures are also closer to the the edge of the flume. Most of POTC's figures by comparison are which are pushed further back into the scene.
That said, as I also said, it is pretty apparent that there's an extra layer of incompetent design that went into this ride too. Even the most basic moving figures are breaking down, not just the animatronics. There have also been lighting malfunctions too. So there seems to be a lot of different reasons behind the failures.