1) Allow coins to be traded. This would be much more balanced and stable than using packs as the primary player-establish currency in the game.
2) Do something about gem gameplays. Since the removal of gems, only the EXTREMELY wealthy players can afford these amazing looking items. Also there are many gameplay items that are either unobtainable or all of them are trade locked. I cannot tell you how much I would like to have something like the silver munchlax coin in my collection. Stop taunting your players with these gameplays, either implement them or remove them. Maybe consider giving a rare gameplay item to players to complete or exceed the limits of the versus ladder.
3) Improve the trading system. It takes forever for trade offers to load. I've always thought it would be cool if you could view how many people have viewed your public trade offer and see who is currently viewing your collection in the trading post. In general, the current trading system is very buggy and slow. The ability for a player to view the average trading value of a certain cards would also be really cool.
4) Make the versus ladder worth the players' time. Nobody wants to grind the ladder for 6 hours to get a trade locked FA plumeria or something else bad. Try a FA cynthia or something. Also I don't understand the point of trade locking cards earned from the ladder. You should atleast be able to trade your FA plumeria for a couple packs on the public trade.
5) Add playmats. Pretty self-explanatory.
6) Make tournaments more interesting. Maybe instead of only 8 man tournaments add 16 or 32 man tournaments. Prizes currently suck, but atleast the packs are tradable. Maybe give out gem gameplays or a rare card as a prize. This is a stretch, but it would be amazing if every month there was a huge tournament where players could compete for championships points towards their world's invite.
7) A ranking system would be fun. Maybe the top 3 players earn some kind of award at the end of each month.
These are just a few of the ideas I have that could improve this game soooooooo much. One of my main fears is that with the removal of gems, most high value items in the game will be accumulated into a few accounts owned by only the wealthiest players. This could become very toxic very quickly. Pokemon is one of the world's largest franchises. Improving your online trading card game would be a great way to give back to your community. If you like my ideas, feel free to thank me with a silver munchlax coin :-P