Background: I just finished kanto, about 50 hrs gameplay.
Things i don't like in PRO:
1. Battling trainers again. I already made a post about this, but i want to touch on the subject again. It's so annoying having to fight level 5 metapods with high level pokes (which might screw your EV as well if you don't expect any obligatory battles). Making the fights optional, as in having to talk to the trainers to battle them again, would solve this problem.
2. As many have already mentioned, the economy is so random. We don't have a reference for prices on pokemon. Having an Auction House will not only solve that, but also the problem of having to walk all the way from cinnabar to cerulean just to trade a poke for 10k (which is more annoying if you have to battle trainers again). You can put a -10% fee or so in the AH as well if you feel it's necessary. If you've played WoW, you can aggree that the AH is awesome.
3. The storage system is pretty bad. We can't even tell what box we are browsing right now. Add some customization in it, like rename boxes, delete/add box, some colors etc. And please show what box we are browsing right now.
4.Leveling up 60+ pokemon in kanto is a REAL grind. I know that all MMOs have grinds but at least it's somewhat enjoyable, this is plain torture. I spent about 20 hours of gameplay just mindlessly grinding exp in seafoam/victory road, just to beat the e4. It was a huge stall in the gameplay compared to getting the badges, and killed my excitement to play the game.
It's a mix of things I don't like/things that should be in pro. I am sure that the staff is already working on (hopefully) all of these and i appreciate that.
A lot of people complain about server stability, but again I am sure it's #1 priority for the staff right now. The game is very new and the progress it has made is amazing.