I think RTD made the absolute best decision to cast Eccleston as the Doctor in 2005.
By the time of the reboot, there were a lot of young people who had never seen Doctor Who, and often hadn't even properly heard of it - even myself, the most I'd seen of Doctor Who was the Daleks in an advert for Kit Kat back in 2001.
What drew me in as a new viewer was this amazing looking series, with brand new characters and fantastic design and story prospects. Something of that would have been lost if McGann had been cast - not because he's a bad Doctor (far from it) but because he came from a bad movie. If you're going to force backstory onto a viewer from the very start it has to be good, and the TVM simply wasn't. If you expect the viewer to be at least somewhat familiar with a character from the very first minute, then that character needs to have been served well previously.
Eccleston was MY Doctor, and remains my favourite Doctor (Smith sits comfortably in second, while my ventures into Classic Who have left Hartnell and McGann warring for third). Part of what made his character so great was the sense of mystery surrounding him, and that is automatically lessened if I know there was a lacklustre film preceding my first experience. I had never heard of Gallifrey, or Skaro, or anything of the sort before - I never saw The Master before 2007 and Dalek was my first ever look at the pepperpots in canonical action.
I do think there is room for McGann to make further appearances in Doctor Who now... the show is well established once again, and I doubt there's a British person out there who doesn't know what it is. But back in 2005, I think the show was hugely dependent on being a fresh image rather than a continuation of one that was a bit stale. It needed the big draw and the modernisation that RTD afforded it, to show people that what had come before the turn of the century was really worth looking back on