This isn't a version of Flight Simulator for the Xbox. It's an attempt to make the existing game fit into a console’s framework, with numerous shortcuts and adaptations made so you can control a realistically depicted airplane straight from the pilot's seat with your Xbox controller.
It's a lot to juggle when you've got the comparative freedom of a keyboard and mouse, or any of the elaborate hardware mockups that serious flight sim fans have put together. When you try to cram all of that into the relatively limited space available on a gamepad, you're asking for trouble.
Having said that, Microsoft Flight Simulator controls fine once you're in flight, but it's the rare video game where I had more trouble with the tutorial than anything else.