Alot of it has to do with Hasbro.They wanted to feature new toy Charchters like every other month so others like Sideswipe, Sunstreaker and so on got left in the wind. Skyfire/Jetfire's figure appears in "Dark awakening"
And many Others, even ones that died in the movie , appear in Takara's Headmasters but that was due to Takara not knowing what The American series had already established.
Den-O wrote: Seasons 3 and 4 had worse animations than Seadons 1 and 2.....
Well Season 1 and 2 was a period of time when all Cartoons in the U.S looked like that. G.I. Joe, He-Man, Thundercats, Jem and the Holograms

. It was Classic animation of that time thats nostalgic for some people (like me).
I love TF Season 1 Animation and I think Season 2 got even more crisp , clear and refined. Season 3 by Far had some bad animation
BUT it also had some of the Best animation of all G1 time. An example ..."Call of the Primitves" That was hands down some of the Best animation of the whole G1 era! ( early Japanimation at it's finest )
Season 4 I felt like they took it back to Season 2 roots of animation but with a whole new look and cast of characters ( hence the Re-Birth

) Prime was back and everything.
But I love the animation of those years, flaws and all!