looking at things in retrospect - storywise - I don't think Season One would have been a good fit for McGann. This is especially so if it began with nothing coming between it and the TV Movie. In the latter, McGann's doctor is filled with child-like wonder, he's soft-spoken, a romantic, and very dapper (especially for a stolen costume). That would be very incongruous with a doctor suffering from shell-shock and guilt following the (believed) genocide of his own race. Maybe if we had "Night of the Doctor" and built on that before Season One, it might have worked a bit better. But given the state of mind #9 was supposed to have, Eccelston had a better aura for it.
And I'm a huge McGann supporter (I think he and Eccelston, and maybe Troughton, were the best "actors" Who ever had) and would love to see more of his Doctor on-screen.