My first Yamaha was a YZ80...in the 70s. My first new Yamaha was a 125cc in 79, an another 350cc in 86. My first Yamaha Boat was an 09 that I purchased new in 2012. My second is a 2017 242x. Nearing the end of the first season on the 242, I can say that it has fewer "issues" than the 09 did. I attribute this to the fact that the 09 sat on dealer lots for three years before being used. Most of these things are a normal 'punch list type of thing' like retighten the bow rales, fix the connector on the leaky center ballast bag, port-side rub-rail fit is off, and there's an off-arrow on the ballast fill bags. As you can see, mostly minor things...
As others have said, you're buying a Yamaha which is a lot like buying a Ford (no offense to anyone that has one). They are good, but are they a Porsche, no. Will they have their quirks but overall for the dollar paid, you get a descent product. For the 4.5 months of the year that is my boating season, I decided on the Yamaha because it's a bit of a Swiss army knife of boats: it can handle the chop of Lake Tahoe (big water), is great for a lazy day swimming, can pull any boarder/surfer out there with ease, and can cruise for over 60 miles in a day (did that last weekend). Is it the best in any one category, no. But overall, it's a good overall do most anything you'd like boat.
One advantage of Jet Boats is their simplicity. They don't have transmissions so that removes a lot. Additionally, on the Yamaha's they are their own water pumps. Again, something less to worry about. You may hear a lot on this forum about "issues" but you also have to realize that this is a place where people come to discuss their toys...and we tend to pay particular attention to said toys. These issues may be common, or they may be rare but over-emphasized based on the overall sample-size of the forum members. However, the good thing with this is that you ALREADY know what to look for when it comes to potential issue and you can stop them before the become a show-stopper.
At the end of the day, if you want a good all purpose boat that will tackle most things it's designed for, the Yamaha's will give you a good return on your investment. You can also take a little bit of pride in that we are not like all of the other boats on the lake. Case in point: up here on Lake Tahoe, you can't throw a Type IV without hitting a blue & white Cobalt (doesn't matter the size). Two weeks ago when pulling up to an on the lake restaurant (where they provide water taxi service) the boat-boy (yes, that's what they're called) said, "Thanks for being in a Yamaha and not a Cobalt...I needed a little variety in my day."
So there you have it, we're not a luxury line, but we're different.
