How would you go about remaking Ruby/Sapphire/Emerald

All the top teams had to either run weather or have a way to stop/handle weather teams.
They were most definitely pineappleing rampant. It's just like stealth rock, sure nobody is forcing you to run them, but you sure as pineapple need every single team to be able to handle them.
If something is so good you can't ignore it, it becomes frustrating, not fun. Weather is now gimmicky, but not bad. You can still make weather work albeit a lot harder and not as effective as before.

XY OU is far more fun than BW2 OU was, so far anyway.

Just went to look at statistics:
In july of BW2 OU politoed remained in #3 spot for usage with Ttar at #8
Yeah, totally not rampant or anything.

Of course top teams have ways to handle weather and SR and common pokemon: they obviously wouldn't be top teams if they couldn't.

Every single pokemon in OU is "so good you can't ignore it" lol. That's why they're OU. You can't just ignore Pokemon and playstyles and expect to win matches. When something doesn't have proper checks or countermeasures it can be frustrating, I'll give you that. However Rain, Sand, Sun, Hail, Hyper-Offense, Stall, etc can all be handled with good teambuilding. The point I'm trying to make, which nobody has yet to refute, is that XY OU has much less team variety than BW2. Losing permanent weather, and the new defog mechanics, make Stall and Hyper Offense a heck of a lot less viable than they used to be. The only teams I tend to encounter in XY are bulky offense or balanced and it's become boring quite quickly.