There's no moving parts with GPS. The one disadvantage to paddlewheels could be reliability. I know you haven't had trouble but it's still an exposed mechanical thing that has been known to get jammed/fail/etc. This was especially true with pitot tubes (that's why there were always 2 speedos). Essentially, your surfing day depends on a cheap plastic wheel on the bottom of the boat. It's not a problem until it is. But of course the same could be said for any component of the engine control...
From my perspective, GPS based Perfect Pass has been the only system that has truly been "set it and forget it", it has worked without a hitch and has always felt like the best solution, but the only downside was expense. I've found non-GPS stuff to be a little for fiddly, or finicky and I've seen plenty of weird behavior with non-Perfect Pass / custom factory solutions (but really no experience with the last 5 years-ish stuff coming from the builders). So I wouldn't put that bullet point for paddlewheels, or at least it's a tie in my book. (again, this is only on lakes, it's a valid point for current)
What would be ideal is a PP system that used the paddle wheel as the primary sensor, with GPS available for calibration and as the fallback control. PP could do all of this in firmware now. And while I'm dreaming, I'd really like PP to implement a hybrid speed/tach based control. Once we're surfing, it could record the engine speed. Then when we stop and start it would already know the target engine speed and could just adjust slightly as needed. Adjusting the response factors, etc and having it "hunt" a little until the speed stabilizes could be so easily eliminated.
2007 Mobius LSV
1989 Sanger Skier DX - sold