As I said a few weeks ago in a similar thread, I think that everyone involved in this era had Good Intentions.
They were all clearly trying to bring the show back to form, with some actually quite good scripts (considering that none of them were TV writers really, just people that Cartmel had met on courses etc.) and a very noble attempt to make the show less... "angry" (for want of a better word) than it had been during the insipid Saward era. And Cartmel clearly wanted to forge a new mythos for the show rather than simply look back at the show's past in a mastabatory fashion like previous eras had become more and more inclined to do.
Also, I've found it very interesting to discover that Cartmel was perhaps the most adept of the script editors at "reigning in" JNT and putting a stop to his stupid ideas (never knew until this month's DWM that JNT was pushing to have The Greatest Show In The Galaxy set at the Doctor Who exibition... Thank f*** that never happened...)
So while - and I cannot stress this enough - I don't think that the era itself was any good (Rememberance, Fenric and [for personal nostalgia reasons only] parts of Battlefield aside), and while - bless them - I don't think that anyone could argue that Sylv, Sophie and Bonnie were particularly good actors, I actually wouldn't change much about the scripts/creative team at all.
Rather I'd change all of the backstage nonsense. Because while the end product was inarguably bad, I'd really like to have seen the Who that these guys were trying to make.
Well, having said that I'd keep the stories the same, actually I'd completely scrap Time And The Rani. Utterly irrideemable in every way (even the always delightful Kate O'Mara couldn't offer a beacon of hope for this bilge) - that scene where Seven wakes up post-regeneration and does a few dreadful pratfalls... that was when Who got cancelled, really, as I can imaging hundreds of thousands of viewers switching it off in their droves. Everything from that moment on was borrowed time. It should have been a more serious story - the first epiosode of a new era is like a missino statement, and while there's nothing wrong with a bit of the daft, or a touch of the pantomime, sticking Time And The Rani first was the production team saying "This is what we're gonna do this time round" - no wonder the show died after that.
Also, on a perhaps more petty note, I think that Whizz Kid was a dreadful mis-step on the part of the writing team. By this point it must have been painfully obvious that only the hardcore fans were still watching. I can imagine kids being teased at school for being fans of the show (hell, I certainly was), and having to make excuses as to why they still liked Who. Only for the makers of Who to throw in a character that was so openly, smugly mocking the only people who were still watching. I wasn't necessarily offended by it, of course, but I do think the second you start taking the piss out of your core audience - who were, face it, putting some seriously undeserved faith in the show by that time, you've shot yourself in the foot and lost all hope you have of winning fans back. Love & Monsters got away with it because the "mocking" of Who fans was sort of an "inside" job - it was writtin about fans, by fans, for fans - we could see things, recognise them, and while we laughed at them, it was friendly and self-depricating. Whizz Kid just seemed... spiteful, for want of a better word.
But otherwise, I'd keep the scripts the same (even Paradise Towers... though I'd probably change Silver Nemesis up a bit so it wasn't quite as obviously "Rememberance Of The Cybermen") and just... do them right.
What the show needed was for the people at the beeb and in the more mundane backstage jobs to give just half a f*** about the show. It needed somebody to take a look at those godawful opening credits and point out how cheap and tacky they looked. It needed a composer who actually made half an attempt to match the incidental music to the tone of the episodes. It needed casting directors who actually read the scripts before just throwing in any old person who was cheap (to take Paradise Towers as an example again, the Caretakers were all supposed to be the people too fat to go to war, the Kangs were supposed to be kids, Pex was supposed to be Rambo... the second that the entire cast sans the Rezzies became bland generic twenty-and-thirty somethings, the entire point of the script was already lost). The show needed effects supervisors who didn't just think "we'll turn the sky pink in post, that'll make it look alien...) It needed to be shot on film rather than looking like it was shot by a bunch of fans on their weekends. It needed a good time slot. It needed the Beeb to actually tell viewers that it was back on the air each season. It needed at least a pretense of a budget.
It needed people to actually care.
If it had been produced better, with a better budget, better guest actors, better effects (note I'm not saying that it needed modern effects, just things that put it on a par with other shows from that era), a better timeslot and better promotion, then who knows - those three seasons may still have turned out to be a bit crap.
But at least the show would have gone down fighting.