It needs constant annual attention in the first place as Steve said. But a huge problem that hasn't helped things at all is that prior to last year the ride had not received a decent refurbishment or proper nightly maintenance in years, having been in an abysmal state of very noticeable neglect (one can only imagine what the underlying problems were guest don't even see). The last time they took it down prior to last year was just to install lap bars on the boats. Little to nothing else was done during that downtime, it was a huge amount of wasted time while they were doing that. I'm guessing that the 2013 refurb was to address the show elements (they got everything painted and the animatronics were spruced up nicely), this round looks like they were focusing on more mechanical issues with the ride system (it looked like they were working heavily on the lift hills, drops, water jets, and likely sensors and computer equipment).
When you go so long without a proper refurb for such a maintenance heavy attraction, issues pile up and you have more work to do to fix things (it ends up costing more in the long term as well). If they took it down for a few weeks to a month per year and did all that needed to be done to keep it working properly like they used to do, they'd not have to take it down for as long. Not to mention conduct better third shift maintenance to prevent things from breaking in the first place. The management running WDW prior to the late 90's did exactly that, and as such it was far more rare to see broken show elements and the refurbs commonly lasted a shorter period of time.