Firstly, just a few comments about the games in the OP:
Command & Conquer
I don't really agree with this, but I see where you're coming from. There's a definite difference between Westwood developed games and EA developed games. That said, Generals was made fully under the EA label - and like you say, it was great. Similarly, Tiberium Wars & Red Alert 3 are both really, really enjoyable RTS games. I think people just gloss over them because they like to think that C&C has gone downhill, but actually if you play them they're a lot of fun. RA3 keeps that campy sillyness in tact from previous Red Alert games and TW is a functional follow-up to Tiberian Sun. The developments since then - with the free to play bullshit - is worrying, though.
Final Fantasy
I don't really agree with this either: you're right that the quality has gone down hill in a sense, but the quality is definitely still there, just dropped. Besides, it's such a huge point of debate - for example, you say games after X was where it went bad, I'd say that X was the game that started making things bad. I seriously don't understand people who praise X and then slate XIII - X was far more linear and had a far more stupid story. Regardless, there has still been plenty of fun to have under the 'Final Fantasy' name since X which cannot be said for some other series out there.
My picks:
Spyro the Dragon
My avatar, my favourite videogame series growing up. Fantastic collection platformers. Then, it all started dropping off. A new developer took the reins, tried to make a game in the style of the first 3, but rushed it and made a frankly broken product at launch (Enter the Dragonfly). Then, a new developer had a go and made a 'decent' game that worked, but just felt nothing like Spyro (A Hero's Tail). Then, we got the 'Legend' series, which was Spyro in name only. Now we've got Skylanders. While I hear Skylanders is actually a decent product, literally any name could've been slapped onto it, it's just not Spyro.
Crash Bandicoot
Same deal as Spyro, really. New developer has a go, but makes a slow and buggy product (Wrath of Cortex). Another sequel gets made that's actually an improvement - I don't have much to fault about Twinsanity actually. But then we got the Titans games, which were fine, but they just weren't Crash Bandicoot. Like with Spyro, I feel like they could've just been any series.
SSX
Same sentiment I've seen a few other people mention actually. It's a hard one to explain. The first 3 SSX games were fantastic arcade snowboarding games. Neon-lit, challenging but fun, beautiful and entertaining. Then On Tour appeared, which was a game I just never got. After the open-world of SSX 3, why were we back to level-based challenges? What was this Napoleon-Dynamite design? Then we had Blur which was fine, but it was basically just SSX 3 with motion controls and no open mountain. Finally, we had the new SSX, objectively a very good game, but just not an SSX game. Everything that made SSX good seemed changed for this new 'dangerous snowboarding' design.
There's a number of series I also thought were starting to go downhill, but they ended up recapturing that magic with later installments and saved themselves. Things like WipEout (Fusion was bad, but then from Pure onwards they were good again), Twisted Metal (3 & 4 were awful, but every one from Black onwards was great), Syphon Filter (3 was looking like the end of the series, but then Dark Mirror revived it in spectacular fashion) and Animal Crossing (I'm still divided on this one. I loved the original, 'liked' the DS version and sort of enjoyed the Wii version. They need to shake things up with it for the 3DS version, imo).
