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I'll repeat what others have already said - get Fire Emblem and Advance Wars.

They're both very attention heavy, and they only allow you to save between scenarios, (which take about 45 minutes to complete on average,) so be aware that these are not good games for when you just want something to do while waiting for the bus.
Just repeating a lot of things said before, but hopefully that'll demonstrate how correct they are.

Castlevania games! I know you said you're not a fan of Castlevania, but I'm interested to know which one(s) you did play, because there have been a few different gameplay styles over the course of the series.

Golden Sun and Golden Sun: The Lost Age if you like JRPGs.

The Metroid games (Fusion and Zero Mission) and the Zelda games (a Link to the Past and Minish Cap) are essential unless you actively dislike those series.
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SimonG: A hidden gem but worth pursuing is "Astro Boy". Trust me.
Yes yes yes. Whoever let Treasure make it was a genius.
Post edited January 01, 2013 by SirPrimalform
Other games that deserve some consideration:
Baldur's Gate Dark Alliance
Max Payne

Very good faithful recreations of their big brother versions.

I also enjoyed Tom Clancy's Splinter Cell on GBA even though it's not quite Splinter Cell.
I really liked that King Kong adventure game, kind of short but quite interesting.

Also, while not technically a GBA game, get the GBC version of Daikatana if you can find it. It's actually quite good. Probably better than the proper PC version.
Advance Wars is ok, and Golden Sun 1/2 are both good.
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Fictionvision: Castlevania Double Pack is probably my favorite on the system. If you are a Castlevania fan it is worth getting as it contains Aria of Sorrow and Harmony of Dissonance. It will probably be expensive unless you find a used one in a pawn shop or something.

Metroid Zero Mission and Fusion. Like before, if you like Metroid, check these games out. Zero Mission is the better game, but Fusion is worth a play through.

Final Fantasy 4-6. Nice remakes with extra content for each. I played through 4 and 5 and had fun revisiting the old games.
How exactly is a remake of the first Metroid better than the newest entry in the series proper?
Post edited January 02, 2013 by anjohl
Some repeats but whatever:

-Golden Sun and Lost Age
-Megaman Battle Network 1-3
-Final Fantasy IV-VI
-Legend of Zelda: The Minish Cap
-Harvest Moon: Friends of Mineral Town
-Metroid Fusion (Zero Mission is good too)
-Castlevania: Harmony of Dissonance and Aria of Sorrow
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anjohl: How exactly is a remake of the first Metroid better than the newest entry in the series proper?
Less linear gameplay. In Zero Mission you are more free to explore like the Metroid series originally was. In Fusion you end up being told where to go by a computer most of the time.
Game & Watch Gallery 4
Advance Guardian Heroes
Bomberman Max 2 (either version)
Crash: The Huge Adventure
Spyro: Season of Ice
Spyro: Season of Flame
Spyro: Attack of the Rhynocs
Legend of Spyro: The Eternal Night GBA
Banjo-Kazooie: Grunty's Revenge (though it's sadly pretty short)
Konami Krazy Racers
Sword of Mana (prequel to Secret of Mana made by Magical Starsign developer Brownie Brown)
Donkey Kong: King of Swing
Mario Vs Donkey Kong (from before the Mini-Marios took over, it's much like Donkey Kong GB)
Yoshi's Universal Gravitation/Yoshi Topsy-Turvy
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anjohl: How exactly is a remake of the first Metroid better than the newest entry in the series proper?
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Fictionvision: Less linear gameplay. In Zero Mission you are more free to explore like the Metroid series originally was. In Fusion you end up being told where to go by a computer most of the time.
Um, you *do* know that Zero Mission is just the first Metroid remade right? So you like Metroid on NES more than Fusion?
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anjohl: Um, you *do* know that Zero Mission is just the first Metroid remade right? So you like Metroid on NES more than Fusion?
While it is a remake, it's more like a remake with liberties.
There's enough different to distinguish itself from its original outing while including gameplay additions from Super and Fusion.

I can't stand playing the original NES Metroid now, but I greatly enjoy Zero Mission.
I do think that, as a whole, it's a better game and more fun than Fusion.
Super is still the best, though (of the 2D games).
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anjohl: Um, you *do* know that Zero Mission is just the first Metroid remade right? So you like Metroid on NES more than Fusion?
Why does it matter if it is based off Metroid 1? The game is using a completely separate engine/graphics/sounds/ect from the NES game and is more than good enough to stand on it's own. Its not like they made this from a romhack of Metroid.

Same goes for games like Resident Evil on Gamecube. Its not a port or HD touch up job, its a completely new game that should be judged on it's own.

Also if I had to pick the NES Metroid or Metroid Fusion, I'd probably pick the NES one as I have more memories of playing it as a kid.
Fire Emblem and Advance Wars have already been said.

I would add the Phoenix Wright/Ace Attorney games, although those are on other platforms so you might have already played them.

This whole thread is really reminding me what a great handheld the GBA was.
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anjohl: Um, you *do* know that Zero Mission is just the first Metroid remade right? So you like Metroid on NES more than Fusion?
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Fictionvision: Why does it matter if it is based off Metroid 1? The game is using a completely separate engine/graphics/sounds/ect from the NES game and is more than good enough to stand on it's own. Its not like they made this from a romhack of Metroid.

Same goes for games like Resident Evil on Gamecube. Its not a port or HD touch up job, its a completely new game that should be judged on it's own.

Also if I had to pick the NES Metroid or Metroid Fusion, I'd probably pick the NES one as I have more memories of playing it as a kid.
Structurally it's identical. So are you saying that the upgraded graphics ALONE make it better than Fusion, which has much better graphics itself than either Metroid or Zero Mission?

I just want to make sure I understand your assertion.
Post edited January 02, 2013 by anjohl
Astroboy: The Omega Factor is one of the better beat'em up games on the system. River City Ransom EX is also worth picking up. If I remember, Dragonball: Advance Adventure is also on the system, and I remember it being worthwhile.
So far ive bought

FF6
ff tactics advance
DragonballZ the legacy of Goku 1&2

Found
Pokemon leaf green which is strangely addictive