It and Holy Terror are probably the most overrated of the BF catalog (with Zagreus being the most underrated), and I didn't love it at first listen, but still liked it fairly much. I only got to love it at a second relisten, where I paid attention to the Nyssa side of the story. Its really basically great.So Spare Parts was okay, but I've heard it mentioned so much over the years as an important story that it was hard to live up to expectations. I didn't find it all that exceptional, really. And I find it silly that it took the "parallel Earth" idea to "Miri"-like extremes of having even the cultural details, names, accents, etc. be the same as Earth rather than just the geology and evolution. I guess the best part was when Nyssa confronted the Doctor over their unresolved issues regarding Adric's death. I wish that had been explored in more depth.
I listened to this one before I'd delved into the Moffat era (it might be one of my earliest audios, come to think of it) and I wasn't as put off but you have a point. I guess its kind of expected in a long-running franchise to see the Doctor as the instigator to the villainous predilictions of his opponents, kinda like Batman's arrival signalled the arrival of all the super-villains and the like. But the way I rationalize it, and I don't know if this helps (probably won't, lol), is that a lot of the villains (not all) would probably had come around to be even without the Doctor. The fact that the Doctor, a Time Lord of a race that seemingly avoids time travel, did so indicates that the reason the Time Lords don't venture off like the Doctor carelessly does, is because they don't want/wish to entangle themselves in unpleasant situations like these (plus the bureaucracy of the restoring things to how they were and the paperwork involved would kill them, haha). Its not exactly the Doctor's fault either, but its a risk he takes for the choice he made to explore the universe in every sense of the word.I found it rather contrived that the Doctor ended up being used as a template for the final Cyberman design. It's the same problem as the Moffat era, making it so that everything in the universe revolves around the Doctor, is caused by the Doctor, is a reaction to the Doctor, or the like. Plus it's a bit contrived to have him at the origin of the Daleks and the Cybermen (and since then he's been involved in two more Cyberman origin stories, and I gather there's one about the origin of the Sontarans too).
But I think the central conflict in Spare Parts for the Doctor is that it meant to be seen more as a follow-up on Earthshock than anything, because Adric's death is still pretty fresh and the Doctor is also willing to completely eradicate the Cybermen from history, which is something he'd never done with the Daleks before then. Its chilling to hear Five be so vengeful, like a post-Seventh Doctor would be under these circumstances. More than anything though, it features a brilliant performance by both Davison and Sutton, who gets to show layers as the lone survivor of a long-since doomed cosmos.
And yes, there is a Sontaran origin story. Its in the Lost Stories range, and its called The First Sontarans, with the Sixth Doctor and Peri. Its a cracking story.