I like both Mysterious Planet and Vervoids - I'd give at least 8/10 for both
Mindwarp is just a mess - In the Colin Baker Years tape, he says it wasn't even clear to him whether the Doctor has been effected by the mindwarp machine and is betraying Peri or whether he is pretending to betray Peri as part of some plan, or whether as we find out in Ultimate Foe, the Valeyard tampered with the matrix and none of this ever actually happened.
Ultimate Foe is a bit of a mixed bag - There's some good stuff in there. I agree the matrix scenes are neat. But, it sort of ends before we figure out what is going on. Somehow the timelords (or some of the timelords) conjured up the Valeyard to keep the Doctor from finding out whatever they did to Earth, but how? And why did they move the Earth and rename it Ravolox in the first place? And what happened to the Valeyard?
Then in Time and the Rani we see 6 travelling with Mel (with no explanation of how he met her in the first place - Wasn't she from the Doctor's future?) regenerate into 7 for no good reason. Overall, I think Time and the Rani is underrated and like the rest of the story, but the regeneration scene makes no sense whatsoever. In the end, I just like to think that there is a whole bunch of stuff in between Ultimate Foe and Time and the Rani that happened that we never saw.
As for JNT, I don't really know anything about the behind-the-scenes stuff. As far as I'm concerned, he produced a lot of great Doctor Who (not every story was great - but that can be said of any era) and that's the end of it.