The typical complaint about using AF lenses on MF cameras is simply the feel, MF lens focus adjustment typically has a smooth gentle resistance that makes focusing manually a pleasure. AF lenses typically have little if any resistance so your fingers don't get the same feedback. May seem like a small thing but it's kinda like the difference between the feel of a toy and a tool. (Both AF and MF lenses can be focused well manually, the quality of the result is not in question.)
The FM2 is a great camera, owned one for a long time and shot a lot with it. The only reason I gave it up was that the automation on the F100 and F5, AF and Flash mostly, has become very important in how I use 35mm cameras.
The FE2 is also a great camera when working properly and actually I prefer it's meter over the FM2 but I've had two FE2s and in both the shutters failed. If I were considering an FE2 again, and needed reliability, I'd be budgeting in and sending the camera off for a CLA before I ever put it into use.