If you are looking at a Merc Seadoo... you either have to do all the work yourself... or find a good Mercury dealer that will work on the sportjets, since most seadoo dealers won't touch them.
Yes... they can be VERY expensive to fix... but so can a modern 4 stroke. Or for that mater... an earlier 1800 with 2 engines. (they normally die together)
If you are looking at a Merc... you either want one that the engine has already been replaced... or find one cheap. The Merc engines are lasting 10~12 years... so a lot of them are getting tired. A replacement power head will cost you +$3500 (for a rebuild) or you can do the labor yourself... and it will be $2k or less.
The jet pump is kind of the same. It's expensive... but it potentially can live as long as the life of the boat, if cared for. The wear ring is a solid part... and is about $400. So... do run it though sand. The maintenance is easy for fresh water. Drain and replace the oil in the main gear case, and stator... and that's about it. If you are in salt... then you want to strip it down some... and put anti-corrosion paste on all the bolts, and moving parts. (that should be done every few years in fresh water)
I use to be anti-Merc... but I love my Islandia, and I couldn't see paying for a twin engine 4-tec rotax.