Really putting me on the spot here, given I've played the vast majority of them (Yes, even Green). If I had to choose, I'd go either Platinum, Gates to Infinity, or Pokemon Stadium 2. Runner ups are Guardian Signs, Conquest, and, of course, Emerald.
:O i've only ever seen one copy of yellow in my life, i'm still annoyed at how you must always have pikachu (it was prob the best way to make money off of the pokemon anime tbh though)
The biggest problem was that you could never evolve the rat. It was easily the most useless member of my party by the end of Yellow.
My favorite Pokemon game(s) were Fire Red & Leaf Green. Honestly, I never really got to start at "yellow" and I had to start them later, but Fire Red & Leaf Green were when I actually starting understanding Pokemon and start to really play it a lot. (I was obsessed with Pokemon for years.. still am kind of)
I remember I downloaded pokemon fire red to my laptop. It was awesome. Only thing I didn't like was thevfact that you had to save the game files from the laptop and not in game. So after the E4 when it auto-saves and goes to the main menu it didn't save. Which means you couldn't continue after the E4 :/
Me I have to say it was either pokemon pearl or pokemon Platine, even though I loved the dongeon misteries