The McGann movie is a highlight ion my collection of Dr Who, and the only real reason why RTD did not ask McGann back has to be because he wanted his own Doctor to start out from the gate and not feature a regeneration at the start or have an handover Doctor in his first series. Thats what I believe at any rate, take it or leave it.
That's pretty much what RTD has said himself. He felt, rightly I think, that it would have been confusing to new viewers to introduce a new character only to have him turn into somebody else 10 minutes in - a lesson learned from the TV movie - and that the new audience wouldn't have any emotional investment in the eighth Doctor, which would render his demise virtually meaningless.