The Concept of Pokemon is AMAZING. It is simple and can literally be fun for all ages if you still have some innocent fragment of your soul. As for the game mechanics, they are very complex with the varying formulas and depth of code. Not to mention the amount of data in tables it takes for 150, 250, etc different Pokemon/items.
now for the nasties.
Battling. Was never quite satisfying. I was thinking that around this time, they would have battles that looked like the intro cutscene(Gengar vs Nidorino) in Pokemon Fire red / leaf green. They are still using same old front back battle images that barley budge.
Game Freak Messed up when they made Silver/Gold. You know why ? It was TOO good. So good that it raised our expectations very high for the future. You can explore Kanto region after beating the johto region !? That was magic, two games in one ! Unfortunately it looks like the multiple region concept was left behind after silver.
Some of the pokemon designs are pathetic. Very few are though. Gen 1-3 are solid original and awesome. i think it is gen 4 that has the ice cream cone pokemon ? That pissed me off.
Another thing was HM navigation. Pokemon that have wings and are a certain level should be able to fly. Pokemon that are water type should be able to carry the player after a certain level. etc. Hm moves always sucked, except surf which was very useful in double battles. Co op would also be nice. Maybe not even MMO (which I know they will likely never do)
