I think from a flying perspective, with proper training and mentoring, you would be fine. I don't know what the insurance market is like these days for low time pilots, but that might be an issue-- I imagine Bruce would know.
A 900 or 1000 would make a lot of sense if pressurization is a concern-- it is a big improvement over the earlier airplanes in that respect. It comes at a cost, as they weigh more, and thus perform a little bit worse, but given your circumstances, I would definitely look in that direction.
In regard to the MU-2, all due respect Dr. Axel, but that is not something I would consider. The MU-2 is a neat airframe with some great advantages, but as a low time pilot it is not going to be easy to operate. I also question the idea that maintenance on an MU-2 would be significantly different, and of course you would need to find someone who can work on it.
If you were going to look at an alternative to the Commander, I would look at a Cessna 441, but I think in the end you would find that the Commander is pretty hard to beat.