It's true that Mary Ann wore short shorts and Ginger wore evening gowns; however, the last season saw their share of miniskirts. Mostly it was Mary Ann gracing the screen in minis, but Ginger put one on a few times herself.
Interestingly enough, the very last scene of the very last episode features Ginger strutting around in a miniskirt, and the girls wonder if it'll catch on. Had the show only lasted another season, it would've undoubtedly been a mini-palooza. We can only imagine what could have been.
Here's a pretty comprehensive compendium of minis wore on Gilligan's Island. Enjoy!
This micro-mini basically replaced the short-shorts in the last season. I'm not quite sure what it actually is, but I'm not complaining, and she wore it a good bit.
Alas, had there only been one more season. Due to rescheduling Gunsmoke, Gilligan's Island was given the boot, and we shall never know the minis of season four.