Best cartoon battle was the battle for Washington D.C. It's different in that the Joe beat back a Cobra offensive, as opposed to taking the fight to Cobra's base.
I found the final battles in MASS and Revenge of Cobra and Pyramid of Darkness lacking upon repeat viewing. They all amount to GI JOE bum-rushing Cobra's base...Cobra commander trying last ditch things to stop them...in Pyramid, they go even further and leave the battle and then there's that space ship thing, which compensates for the lackluster Cobra base with the sonic weapon they fled, I suppose..
GI JOE the movie's one is alright, bizarre though. When you think about the end, the Joes committed genocide on an ancient sentient race. But, uh, not much other choice...since Cobra-La wanted to more or less do the same thing to humanity (The humans of Cobra being useful idiots to help them accomplish that.)
I rewatched most of OPERATION DRAGONFIRE...hard to get through at times. The pacing is slow compared to Sunbow, not nearly as engaging. The continuity is decent with Sunbow and at least CC, Slaughter and Baroness sound like themselves. Cobra's plans are unravelled by roaches short circuiting access Scoop's file....yeah. Interesting to see characters from that era animated. Night Viper used as a Cobra's default troop much of the time. TARGATs making a brief appearance. So many of the 1989 joes ignored entirely...even SNAKE EYES!

Yet, thanks to Python Patrol, Copperhead gets more screentime than he did on Sunbow's run.
One DIC episode where the Joe have a new vehicle the Battle Axe, a axe shaped big tank thing...so Hasbro-like its scary! It's one where Topside, Ambush and Pathfinder join Cobra to find the Joe's security leak.