The fact that there is an in-game shop makes someone a customer, so it doesn't matter if it's free to play or fan made. I would understand that if the game lived off donations, but as of now it looks like a business to anyone, to newcomers even more. I joined a month ago and promptly thought the game survived via micro-transactions.
New players should not have to research information on the forums, when was the last time you played a game and had to read through the game manual? Quality of life changes are present in every modern game, and while there are plenty in PRO (EV's, IV's, etc) there can never be enough! Personally, I always had the forum open because the game itself is a tad confusing. I don't mean that players must be spoiled and spoon fed, but there are many changes that could improve the player's quality of life.
Consumers have always been stupid, and as the years go by, the more stupid they grow. If you've ever worked in retail or with any job involving final customer interaction, you'd know this. You have to expect the consumer to know absolutely nothing about your product, or in this case, the game. I do believed, however, that people that play this game are true fans and are already somewhat knowledgeable about Pokemon, but as I have binged played 250 hours already, I've seen countless posts on the Help Chat that simply scream: "I don't know !$%T about this game."
About OP's ideas, I disagree with the following:
INGAME FAQ: Too much spoiling. FAQ's are usually managed in the game's web site.
CROSS SERVER: It is not necessary IMO. The game's population feels appropriate, and perhaps even amazing. I was truly astonished when I could see at least 1 player in every single map. You don't see dudes in every map of WoW or other MMO's. Two servers allow for easier management for a team, who I believe, despite first impressions, seeks nothing but the prosperity of the game. That means revenue is not their purpose if someone gets me wrong.
I pretty much agree with everything else, and I applaud OP's sincere intentions to suggest improvements to this already wonderful game.
Cheers