It's no great secret that Lawrence Miles has issues with the new series; his blog lets you know in no uncertain terms that he thinks that Steven Moffat is doing things he already did decades earlier, and doing them wrong to boot. (Combined, charmingly enough, with complaints that the production team isn't letting him write for Doctor Who anymore because they have some sort of grudge against him. At some point, you have to wonder if Miles even knows what "people skills" are.)
And yet...I'm doing a re-read right now of Lawrence Miles' Doctor Who novels, and I have to say, if there's one person who could credibly get upset about the new series taking all of his old ideas and doing an extended "house mix" of them, it's probably Miles. To wit:
1) The Time War. It's Number One on the list because it's the most obvious, but it has to be said. In 'Alien Bodies', the Time Lords got into a big war with a mysterious enemy that was also time-active and capable of operating on their level, and they were taking it on the chin. In the new series, the Time Lords had gotten into a big war with a mysterious enemy that was also time-active and capable of operating on their level, and they took it on the chin. The only real difference was that Miles thought that it would be stupid if the enemy was just "the Daleks" at the end of it all. (Mind you, it's easy to act smug if you never had to admit that the Enemy was really the Voord or something.) It's worth pointing out, by the way, that the original plan for the TV show when they weren't sure if they could get the rights to the Daleks was to have the Toclafane act as the destroyers of the Time Lords...and that the revelation that they were the human race from the distant future would have been the big revelation to end Series Three. Worth remembering in light of Miles' comments that the Enemy "came from Earth".
2) The Time Lords. In 'The End of Time', you discover that the reason the Doctor killed the Time Lords along with the Daleks is that they'd become just as bad as the Daleks by the end--the War had twisted them into monsters. Between 'Alien Bodies', 'Dead Romance' and 'Interference', it'd be hard to claim that this wasn't something that worked its way into the popular conception of Gallifrey.
3) 'The Name of the Doctor'. Oh let's see...a story where the Doctor's eventual future death in some vast battle too terrible to be imagined became known to his present self, and in which his future remains turned out to be vitally important to the future of the universe because his biodata--the traces of his entire lifeline--was so special and unique. Huh. And we thought Moffat was dropping an 'Alien Bodies' reference in 'The Impossible Astronaut'.
4)River Song. There's a throwaway line in 'Christmas on a Rational Planet' about Benny's potential child being shaped by exposure to the environment within the TARDIS, and how she would wind up being a potential next step between the human race and the Time Lords. That was a full thirteen years before 'Silence in the Library'. Just sayin'.
5) 'The Runaway Bride'. And speaking of 'Christmas on a Rational Planet', the idea of the ancient Time Lords fundamentally altering the very structure of the universe to make it more fit for habitation by the Time Lords was echoed here, with the "huon particles" that hadn't existed since the beginning of time.
6) The Sycorax. Creepy bad guys who wear skull-masks and use blood control like "a cheap bit of voodoo". You could almost hear Miles' blood pressure racheting up when they showed up on screen.
7) 'School Reunion'. Sarah Jane comes back, but she's older and she's independently investigating a threat to Earth. She gets tangled up with the Doctor again, and winds up discovering that she has a lot in common with his latest companion, who's a fit young blonde woman. I'm not saying that Lawrence Miles was the only person to come up with that idea, but it was a pretty prominent "event" story right before the books lost their claim to being the Official Continuation of Who.
8) The Moffat openings. You know what I mean--'Bells of St. John's', 'The Pandorica Opens', 'The Wedding of River Song'...those really rapid-fire openings that start off with a spectacular set-piece moment that leads into the episode in a totally unexpected way. Now go back and re-read 'Alien Bodies', which opens with the Doctor playing chess with a UNISYC general who tries to have him killed because they found something in Borneo that proves he can die...only to have the Doctor escape by jumping into the TARDIS which is parked sideways halwfway up a building. Moffat was, I don't think there's anything wrong with admitting, influenced by the narrative style of 'Alien Bodies'.
9) River Song escapes by jumping into the TARDIS which is parked sideways halfway up a building. The only real difference is that the Doctor didn't land in the swimming pool.
10) 'The End of Time'. Rassilon's plan is pretty much exactly what the Celestis did. Word for freaking word.
There you go. Ten ways that Lawrence Miles was an incredibly influential figure in Doctor Who on a level all out of proportion to the current recognition he gets for it, and I didn't even mention TARDISes in human form. I think that's pretty restrained of me, to be honest.