I didn't play as many newer games during the GBA era to focus on school, language-learning, and other stuff, but I dunno if I'd agree with GS2 being the best GBA game. I don't even think it's the best RPG on the system. It has some cool stuff like being able to transfer some stuff from the previous game to your current game and the music came out of an era from before Sakuraba started losing some of his touch, and the game itself looks very nice.
But in all honesty, I feel like I've played better games on the system, even if we exclude ports like FF5a, Shining Force, Shin Megami Tensei, Breath of Fire, etc. Plus then you have to start looking at genre separation from SRPGs, console-style RPGs, computer-style RPGs, etc. I feel like comparing SRPGs like Fist of Mars, Super Robot Taisen, or Advance Wars to a console-style RPG like Golden Sun 2 would be a bit weird since I personally look at the two subgenres as apples and oranges. I'm more comfortable comparing console-style TB-RPGs with console-style ARPGs instead. I'm not sure if I can properly count the card RPGs like Suikoden Card Stories on GBA even though I'd like to for pure fangirlism's sake. When you stack the GBA's RPG library against a lot of platforms' RPG libraries, though, you'll find that the GBA's fairly lacking (but that might be due to limitations).
I even think the two Narikiri Dungeon games feel more fun since you're actively doing something in them, and they have some neat job system stuff with customizable jobsets. Narikiri Dungeon 3 goes into an SRPG/ARPG hybrid whereby you're playing on an SRPG plain before you engage in an LMBS battle. Narikiri Dungeon 2 is a straight-up ARPG with job/character classes. They're Tales games so the stories are naturally not that great, but the balancing and job system ideas are certainly there. They aren't my favourite NariDan games, but they are what they are.
Superstar Saga is a more traditional choice to list, but the game itself is balanced and it feels more cohesive and has better dialogue/storytelling than Super Mario RPG in my eyes.
Oriental Blue: Ao no Tengai is a fairly decent balanced Tengai Makyou game. Although it has one core ending, it has a branching storyline system which allows you to take different paths to that endpoint. The story might be influenced by the in-game clock, by what decisions you make, randomly, etc. If you lose against a boss, you can continue through the story, but some events might be closed to you if you lost. However, some events open up to you if you've lost. So it's a game that you can go through time and time again. Skills aren't fixed to certain amounts of damage, so they're useful from the beginning to the end of the game. I think it's one of the best games on the system for its flexibility as an RPG and its replay value.
Mother 3 is still my favourite RPG on the system, though. Really happy I grabbed a copy before they became harder to find. It's my favourite Mother game, and as someone who doesn't wax poetic about Earthbound like many people do, I feel like its storytelling and mini-scenarios via chapter-based storytelling blend together into one cohesive story about the errors of greed and militarism and the overall message that the game is trying to convey about love. Battles feel better when you're trying to figure out the battle track's rhythm to score more hits. It's also a very good looking sprite-based game to me.
If we're looking at straight-up GBA game, I still can't make a good assertion for that one best GBA game since I'm still catching up. I played Metroid: Zero Mission and Metroid Fusion a few weeks ago for the first time, for example, and enjoyed Zero Mission and its extra mission a lot. It gave me a lot of what I wanted out of the original Metroid and didn't have the oddball pacing that Fusion had. Oscar was mostly right when he said I'd like it more than Fusion.
At this juncture, I feel like my favourite GBA game is Mother 3 because of its writing. But there are lots of stuff I like on the system. The first Boktai is very good, Puyo Pop Fever is super-fun, some of those RPGs I listed above are great, Ninja Five-O is great, the Harry Potter GBA RPGs by Griptonite were decent, Mega Man Zero 3 is good, The Minish Cap is nice to look at, Astro Boy needs a once-through, and the Sonic Advance games are decent outside of the last one.
I haven't played the Megaman Battle Network games past the first one, but I feel like they wouldn't jive well with me despite being a big Mega Man fan. I tried the first Star Force game and I still haven't beaten it even though I'm at the end and from what I can tell, the BN games are similar to the SF ones.
So... while Golden Sun: The Lost Age may not be best on the platform, it's among the better RPGs on the platform but it is not the best game on the platform to me.
