Well there is an easy answer for why season 3 is as long as it is, syndication. At the time there was a push to make as many cartoons at least 65 episodes long as quickly as possible, this is because you can air 5 episodes per week for exactly 13 weeks, which is more or less three months. Normally a show aims for 100 episodes to achieve syndication but 65 is enough and more typical for animation. It is why:
- Batman: The Brave and the Bold
- Pepper Ann
- Adventures of Sonic the Hedgehog
- Ed, Edd n Eddy
- Chip 'n Dale: Rescue Rangers
- Lilo & Stitch: The Series
- Peter Pan & the Pirates
- Teen Titans
- Spider-Man: The Animated Series
And many more have exactly 65 episodes.
As for season 4? Who really knows? Maybe they decided to go for 100 and overshot it a bit? Maybe they initially intended to have a season that would air one episode per week for exactly a year? Maybe they weren't sure of how many episodes they had and wanted to be sure they had enough? Maybe they were afraid Mirage would license the property to someone else if they didn't have back up episodes they could air (which to be fair, kind of happened)?