Sorry if this is considered necroposting, but I seem to have found the flags that determine the extremely harsh sunlight in Omega Ruby! (Yeah, I played through the game again just to get to that part. lol)
Not sure if it requires un-ticking the Defeated/Captured Groudon flags, but if you set flag 2809 and un-set flag 0458 in Omega Ruby, then the extreme sunlight will return to eastern Hoenn once again. As of yet, I don't know if the same flags control the heavy rain in Alpha Sapphire. I'm about to test that soon.
Edit: Surprisingly, modifying the same flags in Alpha Sapphire makes it extremely harsh sunlight just like in Omega Ruby! Interesting... I'll have to figure out the heavy rain flags another time. (Unless you guys are willing to do that for me... Lol!)
Edit 2: I managed to get the heavy rain working! The flag to enable is 2810, I think. Enjoy getting soaked in heavy rain!
Screenshots:
P.S. I don't think it's necessary to un-set flag 458 to get the primal weather...