I have an Innova and I know only too well how easy it is to swoon over them. I bought the dealer's demo model. I do not have micro handles and I would say I have done some pretty detailed quilting. The beauty of micro handles is you can always add them way far down the road. You don't need to have them put on at the factory or anything like that. Some people have just adjusted where their regular handles are.
Mine has taken any thread I have thrown at her. I only had issues with Superior Rainbow thread and that was only because my tension was too high (that thread doesn't like much tension). My favorite threads to work with are Glide and Isocord. But I have used Bottom line, sew fine, king tut, Rainbows, Highlights all from Superior, YLI, Connecting threads essential pro (their poly) and their essential cotton. I have even used some serger thread my MIL picked up at a yard sale with no issues. So I would say you can use ANY thread on an Innova.
When I was purchasing I almost got an HQ until I test drove the Innova and that was all she wrote.