Ask mechanic why he didn't rebuild other engine at the same time since he is recommending it now and why the other one was rebuilt in the first place, also how many hours since the rebuild of the other engine and the carb install, could just need new plugs. I had issue where plugs were fouled and caused similar issue to what you are having. This will all help you get a good baseline of the overall condition of both engines and what may or may not be needed in the future. All mechanically records and dates you can get your hands on and how many hours it's been run on average. This is just all good to know information that will help if you move on to another mechanic or start to take on some of this yourself.
Keep using the good oil (XPS), and NO-ethanol 87 octane fuel, winterize it properly, replace plugs every couple years and she will last a long time, these engines are tight if they are taken care of. I have two other PWC's with the same engines two years older still on original engines. Don't skimp on oil, never use anything but 87 octane NON-alcohol fuel, keep an eye on oil level and engine bay regularly to make sure things aren't leaking and it's using oil at the proper rate(manual says 50:1) Grease the drive shaft regularly every 3 tanks of fuel roughly. I still get 45 - 50 mph at 7000RPM but I normally cruise at 5000 -5500 RPM which equates to about 25-30mph depending on water conditions and burns about 10-12 gallons per hour at this cruise rate.