This has been an ongoing issue for me since last year. It doesn't keep us from riding, but it is super annoying and I assume can be fixed if we can figure out the problem.
The problem is that it seems to be completely random and intermittent. Basically I'll be driving and the boat will slow about 1/2 mph or so then pick back up. You can hear it "bah, bah, bah, bah" just a little while it does it. Sometimes we'll ride for weeks and no problem and sometimes it happens everytime we are out.
Last year when we had the issue I posted on here did what was suggested: fuel injector cleaner, isoheet, new fuel filter. I've had it at 2 different shops, including the dealer, and neither could find anything. And I know if I pay to have them come with me on my boat so they can experience it, it just won't happen because it is intermittent.
The only guess I have to pinpoint when it seems to happen more often is when I have the boat full of lots of people or when I take on lots of water (like yesterday I was in neutral picking up a surfer and another boat turned into me and sent huge rollers over the back of my boat) Immediately after that roller, I noticed the hesitation.
It seems like it could be a fuel/water issue, but I had this same problem intermittently all last year too, but when I checked for water in the fuel there was none evident.