Thank you for making this great game. I've been enjoying it a lot but I also believe every game has room for improvement. So here are my honest opinions and I hope they may help you in making even greater games.
1. The use of berry
It is usually optimal to use just one type of berry:
a) There is little to no card draw manipulation in this game, and the opportunity cost of drawing an unusable pokemon due to the mismatch of berry colours is just too high.
b) The berry costs of some pokemons are still single-coloured after adding glyphs. It's not hard to build a single-type-berry deck.
c) Though it limits your choices of pokemons, type advantages mean very little to this game. +1 damage is insignificant when a pokemon is dealing 5 to 10 damage each turn. The absence of type resistance further diminishes the importance of type diversity.
2. The progression system
At every stop, players are given 2 to 3 choices. This restriction doesn't seem to add a lot to the gaming experience, as players are always allowed to turn back when they reach the gym, meaning that every type of choice can be made available given that the players keep turning back from the gym.
Thus, this restriction doesn't really do its job but makes the game grindy instead. Sure players can choose not to grind. But there is a saying, "given the opportunity, players will optimise the fun out of a game." Understandably, players would want to create the strongest team they can before they battle the gym leader. If they want to do so, they would have to keep turning back and grind until the desired choices appear.
I usually have more money than I need throughout this game, as the battle nodes tend to appear more than the evolution/tribute nodes.
Since all nodes except the free money/card nodes have a cost to take, be it money or a pokemon, it makes sense to remove the free money/card nodes and allow players to choose whatever nodes they want.
3. The minimal deck size requirement
Once again, due to the lack of card draw manipulation, it is usually beneficial to keep our deck size minimal. However, beating a gym seems to increase the minimum deck size by 3 every time, forcing us to use more pokemons, and thus train more pokemons.
Without the freedom to choose whatever nodes we want, it is quite grindy to train new pokemons. And since type advantages are almost non-existent, it does not feel rewarding to train new pokemons too.
All in all, thank you for your effort. I would be thrilled to see any new game coming from you.