Well, the abilities Blaze, Overgrow and Torrent won't work, as well as Swarm if I remember correctly. Weather won't be boosting moves as well. Hidden Power and Weather Ball won't be working properly.
I originally wanted to change the 'mons whose abilities are affected (Charizard would have Intimidate instead of Blaze, for example), but I'm really not sure if that would be a good idea. :/
Is this a common issue with every hack that has the split?