This made me think hard about what the best GBA game really is. I came to some sort of tie between Metroid: Zero Mission and WarioWare Inc Mega Microgame$ and Advance Wars.
Honorable shout-out to Astro Boy: Omega Factor.
I haven't played Drill Dozer.
For argument's sake: I wasn't a big fan of Metroid: Zero Mission. It was my first Metroid game and I found it too hard and confusing (it was a long time ago), so I used a walkthrough. I don't seem to remember liking games on which I used walkthroughs (this includes Mega Man Battle Network 4). I was a bad gamer :/
Never played WarioWare Inc
Advance Wars (along with Fire Emblem and M: ZM) falls under the category of "Game I liked until it got too hard." I couldn't beat that level where the green team is introduced (the airplane-heavy guy) and didn't pick it up since. I tend to be bad at strategy games, with the exception of FFTA. I suppose, since again, it has been quite a while, if I gave Advance Wars another run I could probably get further.
I did like Astro Boy though. Maybe if it wasn't so short I would have kept it.
So in closing: FFTA is definitely top of my list, I had a lot of fun with it and should probably start playing it again soon. I really liked the job system, although I didn't figure out how to use it until a good ways into the game, so I could have had my four deadly ninjas much earlier on.