Hey Jordan,
I bought a 2002 Sea Doo Utopia 185 Sport with the 210 HP carbureted motor last February (they had the Distinctive and Sport models in 2002, the Sport was the newer hull and trim colors that ran from 2002-2004). So I have the identical hull as your boat and spent all boating season last year getting used to it and enjoying it. I previously owned a 1996 Sea Doo Challenger for seven years (great little boat) so I wasn't new to owning a 2-stroke jet boat.
I was surprised at how much smoother and quieter (quiet is probably due to the engine being covered much better in this boat than the Challenger) the Mercury was vs. the Rotax (don't get me wrong, my experience with the Rotax was nothing but great, I would definitely own a Rotax powered machine again). I feel very little vibration at idle and absolutely none at WOT in the Utopia. Now I know that we don't have the same motors, but I see higher speeds on my speedo and do not experience any vibration at WOT (I would think your injected motor would be smoother than my carbureted motor). Last season I regularly saw 50-53 mph on the speedo (I broke out the GPS once last year and while seeing roughly 52 on the speedo I saw 48 on the GPS) and the number of riders really doesn't seem to affect top speed too much (these boats leap out of the water and on plane and have plenty of power in my opinion). With that said, I think you may want to give everything a good look over and possibly throw a new set of plugs in it like Dr Honda suggested. BTW, I just threw a new set of plugs and wires in mine last night (NGK BUZ8H off eBay, 6 plugs for $26 to my house, was keeping my eye out for a great deal and found these over the winter) and worrying about the age and condition of the wires after handling them I also picked up a Magnecor KV85 wire set (Magnecor wires are one of the best out there, pure silicone jackets, the last set of wires you'll buy...Magnecor P/N 65218, although I think you have different coils and might need P/N 65131?), I highly recommend the Magnecor wires, a little pricey, but they'll outlast your motor (I previously co-owned and operated an automotive performance shop for some time during the 90's and was a Magnecor dealer if you couldn't tell, along with being a Vortec dealer until ProCharger came out with their intercooled blowers, then we became a ProCharger dealer...sorry, I tend to ramble sometimes).
Now that I've written a book, I guess what I'm trying to say is that I think you may have something a little off with your boat and I'd give it a good look over. Jet pump, impeller, plugs, etc...
I only use the Quicksilver Premium Plus oil and run 91 octane fuel from either BP, Mobil or Shell (not looking to start any debate as to whether or not higher octane fuel is better or just a waste of money...just want to share what I'm running through my motor, which runs quite smooth). Here in Michigan gas dealers used to have to label their pumps with a tag if their fuel contained ethanol (ethanol bad...again my opinion, but it's not hard to find things to support it) and BP, Mobil and Shell were the only dealers that did not have ethanol in their fuels here. Unfortunately the law changed and dealers no longer have to identify their fuels as containing ethanol so I continue to use the brands that previously didn't contain ethanol in hopes that they still don't.
Love my Utopia and I'm sure you're going to as well. Just wanted to share my thoughts on your vibration concern, hope everythings in good order for you and enjoy the boating season!