Little Cup
Little cup was the weakest area that had the most potential, but I imagine that the systems that would make it cool are just not supported yet, which is understandable.
However, it would have been way nicer to not have to beat the elite 4 in order to take a whole team of level 25s in, and have a move tutor who can teach us higher level moves, like you would be able to use in Little Cup. This has potential, and I'm hungry for more, but it needed work. Not being able to access your box in the LC area was really bad too. So basically, if you went to do the LC content you had to stay there until you absolutely were done with the e4, and leaving would (presumably) make you start from scratch. That felt really bad, so all I did there was the shaymin quest part.
In a perfect world where you guys have infinite resources (and I know you don't, don't worry), a level sync down to 25 in the area would have been cool and solved most of the problems. However, I'm willing to bet that such a system isn't supported yet, and is pretty low on the TODO list, so I understand why it wasn't implemented yet. It would open up so many possibilities for low level such as actually having EV trained mons with their full moveset.
Shaymin
I liked the shaymin quest otherwise, it was jarring for me to have to figure out the giant puzzle of the island but it was satisfying to figure it out. I guess that's the difference between a game that hands you everything and a game that makes you work for a reward. I think I overall liked it, but maybe there could have been more things that showed you whether you were doing the right thing, or whether the things you were doing were actually helping you on the quest. Overall, the idea was still nice. I waited all year to get a shaymin and now I have one and I love it.
The tropius part of the quest I really only figured out with faith that what I was reading from dialogue was correct. I imagine others who had to contend with the same 5% drop chance for two bananas would have probably been wondering after an empty 5th Tropius whether this was actually the correct method.