The first game that comes to mind for me is Civilizations 4. I’ve probably spent hundreds of hours playing but after getting used to 5 and 6 I have a really hard time going back. Going back and forth between 5 and 6 I need to rethink some strategies but with 4 I feel like I need to rethink everything. I don’t know if it’s because of the tech tree layout in combination with the civics system, things like unit stacking, or maybe just a bunch of little things but it takes me a while to readjust.
Pikmin 2.
There are a couple of bosses in that game I absolutely hate to this day and do not like whatsoever. One returned from the original and one is a variant of it. Every game has had a variant of that shall which not be named. Any other arachnophobes probably know what I’m talking about without needing to mention the name.