[Again, spoilers follow] I dunno, I think the 2006 final was very well done (of course it still suffered from that stupid "touch to open" crap). It wasn't perfect, but it was much better then 2005 and this 2007 one. In the TV movie it is clearly expressed that the Master has used up his 13 regenerations - so why should he have even been able to regenerate again?
I also speculated ages ago that "you are not alone" does not mean there's only one other timelord. I don't know if they just want people to believe it's just the Doc and the Master... but I speculate there are more timelords then that. And as I said before, the sonic screwdriver can't lock a deadlock; and if the Doctor could unlock the coordinates so could the Master. The Master isn't stupid and once had his own TARDIS, if the Doctor could unlock it so could he.
You can't leave out the Doctor all episode - it doesn't work. Doesn't really work as a 3-parter either, it should have been a 2-parter (with the "Utopia" occurring earlier in the series).