Why are some rides that are no longer around so fascinating to people? I agree -- it all comes down to the ride replacing something that people liked more. The amount of people who wish for the old ride or attraction is related to how accepted the new ride or attraction that takes its place is.
In the case of the PeopleMover / Rocket Rods, the attraction was replaced with nothing, so they have an understandably large following because when you look up at the empty tracks, it is hard to say that nothing is better than something, which is what we had before.
In the case of the Country Bear Jamboree, the general feeling is that Pooh isn't very good, so the bears would be better. Having said that, you hear a lot less about how people miss the CBJ than the People Mover, because there is at least something there.
I think ATIS is an odd duck only because of the type of attraction it was not being replicated. A science-based attraction involving you supposedly shrinking is quite unique, and although HISTA is sort of the same concept, it isn't nearly as interesting as the ride itself was. Having said that, the love for ATIS seems to be a lot stronger now, years after the closure than it was when they finally decided to shutter it.
In the Eastern parks, Alien Encounter is the perfect example of this. I loved AE, but it was obvious that the ride wasn't loved by many that went to WDW, and something needed to be done. Now, people talk about how great AE was only because of how bad the replacement is. If AE had been replaced with something of the caliber of even Star Tours, I don't think that anyone would be crying for it to return.
Perhaps the best example though is Journey Through Imagination's transformation. They took a ride that had what was more or less the mascot for the entire park and they decided to remove him from that attraction and replace it with something that was a little too scary for kids, and a little too dumb for adults. So, you have millions of Figment plush, toys, figurines and whatnot on people's desks and in homes across America as a constant reminder of EPCOT, and then when the family finally goes they want to see the dated, although still really fun ride featuring their favorite little plush toy only to find out that the ride is completely changed, and the new one makes no mention of this little guy.
To me, it would be like pulling Mickey out of the parks and saying that it is an upgrade.
But JTI is an issue where, unlike most rides, Disney literally decided to remove a character from an iconic ride where he could not be found *anywhere* else, and he had been so popular. Hell, I have a Figment on my desk at home. It was a complete mistake, and people are definitely obsessed with that because Disney got people to buy into the character, only to pull him completely from the park.
Overall, the obsession is no different than people saying they would rather see the old things instead of the new. In your example, if your option was to watch TMNT or a really cheap, thrown together cartoon that made less sense, which would you wish you had back? Or if the option was TMNT or the old school grey fuzzies? I'd vote for TMNT every time because even though it might not hold up perfectly, it still ultimately is a lot more fun than nothing.