Cushions have a way of flying out of the boat if towed without a cover at highway speeds, even cupholders can come out on occasion as those speeds make for some pretty big pressures in some weird areas. I have never heard of bent wheels...except where run over curbs or dropped off a curb. I have read about really good customer service and some pretty lousy customer service over the years about Yamaha. I hate to say this, but there are always two sides to the story. I am not doubting you, but if you didn't include in writing, on the deal sheet and again on the closing papers, that the shipping cover was included, many of them just trash them. Other dealers give away the shipping cover. But without securing all loose things in the boat, carpets, cushions, literally anything that isn't locked down, towing without a cover is risky.
I would certainly agree that you should go straight back to the dealer, with the boat, and get the wheel issue sorted out, no matter who damaged the wheels, they have to be straight. But your idea of straight may be different than what trailer tires and wheels typically are. They don't come balanced, but some have them balanced anyway. They are bias ply tires, not radials, so they don't balance well. Others change out the wheels and tires quickly, others wait until they are worn out. If you can prove that you drove away with wheels that were not true, they should stand behind them. But my guess is that once you have made it home and back, they will pretty much feel that any damage was caused by you. If they are typical wheels and the tire place just couldn't get them to balance and made excuses, which they often will with bias ply tires, your on your own. The dealer may help with some of it anyway if they were delivered to him that way. Get with your salesman and the service manager, maybe you can get some help with it. If you were promised a cover, and they didn't have it and were going to get it for you later, I would say you have an argument about the cushion too, as they are prone to fly out. A dealer should attempt to make your purchase experience a successful one if you are workable too.
The dealer I bought my second boat from promised me a shipping cover too, since the one on the boat shredded in the first 30 minutes of driving. But I had bought a mooring and trailering cover from them as well, so I just put that on and finished my 300 mile drive from getting the boat. I didn't intend to tow the boat with the new cover at that point. I never received the shipping cover from the selling dealer, and bugging them about it just became work, so I stopped. And that wasn't in the deal sheet either, because the cover was on the boat when I left and it shredded. The promised cover was nothing but a phone call that didn't materialize. Best thing I can share with you is to put expectations outside of the basic deal behind you, and enjoy the boat without letting this set the tone. If you have to have true rolling wheels to be happy if they are just what they are, go get some wheels and radials and be done with it. Many of us drive with the bias ply tires and stock wheels for 1000's of miles without issue, so if yours are really bent and it isn't from a curb or something similar, get them to ride with you and see it, they should replace them.
Please do update your profile as mentioned by
@Julian to include your location and new boat, it will help you going forward. A good many guys have found a number of solutions to stock wheels and tires that they just didn't feel were true enough for them, start a thread or search for wheels or tire replacement, the options are many. One more thing that will help you from scratching that beautiful boat...practice. Many folks just load up the kids and neighbors and hit the lake, only to have distractions and crowded ramps haunt them into damage right off the bat. These boats are different than other boats and nothing like the skis you had, except to have jet propulsion. They don't handle like the skis at all and they are big and have a bunch of mass. They are easy to maneuver only after you learn to predict what they will do in varying conditions. So a weekday without the masses, and your first mate, will learn the nuances and behavior, to establish the skills you need to have a great summer with the new boat. Use lots of fenders the first month, practice loading/unloading before you ever leave the ramp and do this on a CALM day. Practice docking skills in open water, again no wind, with either a buoy or a fender floating. And after the break-in period, and you get to mash those throttles all the way down, get your first mate to snap a few pics of you at the helm...we love pics here! Congrats again, and don't let the first experience set the tone, much enjoyment to come!