One thing I've found interesting is that a few Pokemon like to be petted in places right next to "dangerous" spots. For example, Bisharp likes being petted down the middle of the chest, right in between blades that can hurt you. Heatran likes getting its metal leg braces rubbed, but these are again narrow areas surrounded by burning lava. I also find it amusing that Pokemon based off the same animal seem to prefer/hate the same spots - all the fox Pokemon seem to love getting their ears and their crotch rubbed (I've actually noticed a lot of Pokemon like the latter, XD), for instance, whereas all the cat Pokemon don't like ear rubs (Espurr especially hates them, although Purrloin may be an exception).
Another thing I've had a hard time figuring out is how the gift system works - you know, how the three Pokemon who visit your Amie screen give you a present after a while. The first time I ever had Pokemon visit, I had one of the fancy seasonal Poke Puffs out, and got one of those special brown Pokepuffs back. I've tried this again with the same kind of Pokepuff later on, but just kept getting generic things like decorations or lower-grade Pokepuffs. I also haven't seen any difference depending on what grade of Pokepuff I leave out, and I've also been receiving presents when I had no Pokepuffs out.