The biggest difference is like you said, one still makes jetboats while the other does not. Long term this could be an issue with parts availability for non-engine items. FInding a place to service the Doo boats can also be a but difficult to find, but they are out there.
The reverse system on the Doo is way better IMO and Doos are generally cheaper than the Yamahas, but that's for the reason stated above.