If you like Strategy games and Tactical RPGs then I have some recs for ya. Other then that I don't play my GBA all that much.

Advance Wars - Turn based modern warfare themed strategy game. Graphics are a semi anime style for the characters and the units themselves like kinda chibi. There's all sorts of neat units to command and special abilities the officers you play as have to spice things up. The game can also be very challenging.

Fire Emblem Series - I adore this series. They are tactical RPGs a la shining force. You level up your units and promote them to stronger types. I've beaten the 2 US GBA titles multiple times each. Good story, likeable characters. Can start off challenging but if you do well it gets easier as you progress. It is quite satisfying to see the units you've worked hard leveling up kicking enemies ass's later in the game. The 2nd game Sacred Stones, while also quite good is rather easy in comparison to the first Fire Emblem. The stories between those two are unrelated so you can play either one.

Yggdra Union - A bit of an oddball strategy game. There's a bit of a learning curve at the beginning to understand how unit placement works and making your attacks successful, but once you've learned how it works it's a rather simplistic battle system. Awesome soundtrack and humorous attack sequences make it worth a look.

Sigma Star Saga - Another oddball game but rather good. Combines Sh'mup and RPG elements. You explore dungeons searching for upgrades for your ship like different bullet types etc. You'll get summoned into random battles during dungeon sequences where you're transported into a ship and then you play the game like a shooter until all the enemies have been defeated. It sounds weird but its actually pretty cool. I only beat my copy recently though i've owned it since it came out. lol.

That's what I've got for you. Feel free to check em out on youtube, wiki or whatever and pass your own judgement.

I looked through your lists pretty quick and I figured I'd throw in my comments regarding some of the ones I've had some experience with.

3DS

Sonic Generations: I've read that this one is pretty different from the console versions, so I can't comment too much regarding this one. I played the PS3 one, and it was honestly one of the best Sonic experiences I've had in ages (and I was a pretty hardcore fan). If it plays even remotely like the console one, I'd say try it out.

DS

Kirby Super Star Ultra: Definitely yes. It's one of the best examples of a remake done right that I can think of. It's enhanced in almost every way and even has some new exclusive stuff to do. I can't recommend this one enough.

Kirby: Squeak Squad: I feel that this was one of the weakest Kirby games I've ever played. It's okay, but it reeks of average and there really isn't anything special about it. It has some interesting mechancics, but I felt that none of them were really taken advantage of. If your a fan, I'd say try it out, but I'd get Super Star Ultra and Canvas Curse before picking up Squeak Squad.

Kirby: Canvas Curse: This was one of my first DS games and I've had a lot of fun with this one. There's plenty of stuff to do and unlock, so there's certainly some replay value. A lot of the remixes used were pretty awesome as well.

GBA

Metroid Fusion: I'm a pretty big Metroid fan, so I enjoyed this one a good amount. I won't lie though, it is a fairly difficult game and there will be a few occasions where you will get frustrated playing this.

Metroid: Zero Mission: This is a unique reinterpretation of the first Metroid. Quite unlike the original game, this one is easily the easiest Metroid game I've ever played. I suppose it's a good starting place for newcomers, and it's worthwhile to play through once I think to see some of the story and new stuff, but I'd personally put this on a little lower tier because of how easy it is.

Kirby and the Amazing Mirror: This game's okay. It's got a unique exploration element to keep you playing for a while, but unfortunately, once you have found all of the treasure, there is little reason to play this game again. I didn't enjoy this one as much as Nightmare in Dreamland, although it's certainly not a bad game.

Wario Land 4: I really enjoyed this platformer. It mixes up some fairly challenging platforming along with some unique puzzles to spice things up a bit. The boss fights were fun, requiring a specific strategy to defeat. I recommend.

Castlevania Double Pack: Move this to your top tier. No, seriously. They are both at least solid Metroid type games. Harmony of Dissonance is an solid game. It has pretty impressive looking graphics, although in exchange the sound had to take a hit; the music quality is more like what you would expect from a NES game (not that it's bad, it'll sound much different from what you may be used to on a GBA game). Aria of Sorrow though is easily one of the best Metroidvania games you can get, second only to Symphony of the Night, in my opinion. It has a very interesting weapon mechancic were you can capture a enemy's soul to use as one of three types of abilities: there's your Bullet type, which functions as an alternate weapon; Guardian, which can offer some different abilities that must be activated to use, such as shield or a high-speed dash; and finally you have the Passive abitilies that's always in effect as long as it's equipped. The music, like most other Castlevania games, is really good. So move Double Pack into your top tier, I can almost assure you that Aria of Sorrow alone is well worth it, although Harmony of Dissonace is also an alright game.

Some of my own recommendations include.

DS

Castlevania: All of the DS Castlevania games are very good. Dawn of Sorrow and Portrait of Ruin are pretty good Metroid type games with similiar gameplay. Dawn of Sorrow is a lot like Aria of Sorrow in gameplay mechancics, since it's a direct sequel, and Portrait of Ruin is pretty similiar as well. Order of Eccelsia is a pretty difficult game, since you can't just grind and expect to win, it actually requires some level of skill to beat. It's more like the classic Castlevania games in that fashion.

Castlevania Circle of the Moon: The second best GBA Castlevania game. This one is actually fairly challenging and has a very unique magic system in the form of mixing and matching one of two sets of cards, a element card and a effect card. Certain combos would merely change the element of your whip while some would change it into an entirely different weapon, some would create shields, projectiles, you get the idea. Music is awesome, much like the rest of the games. The only real complaint I have is that the graphics are on the dark side, but since you will be using a console that has backlight, this won't be as much of a problem.

Mario Kart DS: A very good Mario Kart experience, probably my second favorite only behind 64. Plenty of stuff to do, so there is a good number of replay value. May not be as worthwhile to you though, since I see you have the 3DS version on your list of lower tier wants.

GBA

The Mario Advance games are pretty good remakes of classic Mario games. If you haven't had a chance to play any of those, the Advance games are pretty good alternatives.

WarioWare Inc. Mega MicroGames: This is a video game, pure and simple. It's one of my favorite games to play when I'm bored and don't know what to do. The premise is simple enough, get as far along playing a series of 3-4 second minigames for as long as you can. The speed and difficulty go up as your progress, so it stays challenging for a long while. Ridculiously fun.

I may add more when I have more free time to kill.

I had a GBA but the only game I played for a significant amount of time was Megaman Battle Network 3, which was excellent. Best one out of the six or however many there were.

Harvest Moon - Friends of mineral town is decent too, and its starting to rise in price for some reason. Not sure why, its not rare.

The DS however, I play tons and recommend the following regardless of whatever price you find it at:

Bomberman DS 2 - We've been through this

Wario Ware Touched - My favourite WarioWare, superb minigames
Mario Kart DS - Great fun, and not as gimmicky as MK7

Yoshis Island 2 - My favourite platformer on the system. The game is big, the visual style is lovely, the music fitting and the whole thing plays great

All of the Ace Attorney games - Preferably in the correct order

Rhythm Paradise - You need a sense of rhythm for this, watching my Ex fail repeatedly at it was amusing. Some of the songs you have to tap along to are crap but its very fun nonetheless

Mario & Luigi - Bowser's Inside Story - The dialog is superb. I would say this is the second funniest Nintendo game ever, behind Paper Mario 2.

If you can get it at a decent price, maybe also consider the following:

Anno: Create A New World - A good strategy game that works well with the controls

Space Invaders Extreme - Awesome visuals, great soundtrack, tried and tested gameplay with power-ups thrown in. Classic stuff

Metroid Prime Pinball - Accurately themed to MP1, good solid pinball fun

Tetris DS - Tetris on the DS

Scribblenaughts - A clever puzzle game allowing lots of variation in how you solve things

I can't believe I forgot to mention this one. I second this, since it's a pretty good variant of Tetris with cool NES game remixes with some interesting game modes (I like the Classic one, of course, but I also liked the, what I believe was called, Catch mode (it's the one with the Metroid theme) that was really fun).

How did I forget those too?! Put me out of my misery. I've only played the first two, but they are awesome visual novel kind of games. The characters are quirky in a funny way, and there is quite a bit of good writing in there that will make you laugh despite the rather dark premise (you are trying to defend your clients in what are all pretty much murder cases). The only real bad thing about them is that, since they are visual novel type games, once you've finished all of the cases, there's nothing left to do on them. Well worth checking out, though!