I've had a Game.com since it was released in '97 and have a good majority of the entire game library. You've got to be joking when you say that Fighter's Megamix, Indy 500, and MK Trilogy are -better- or even -on par- with GBA games. I've seen better animated GB games. Here's a good lowdown on what does and doesn't suck for Game.com.
Indy 500 - Complete trash. The actual images are nicely presented, but the animation and movement is on par with one of those LCD Tiger handhelds. I'm not kidding. The gameplay is terribly boring and unfair. Yuck.
Batman and Robin - This is actually a decent game (decent, though). It's basically a side-scrolling beat-em-up (think Batman and Robin on the Genesis, but much slower). Progress forward, punch some enemies, progress forward, kick some enemies. There are a few stages where you throw Batarangs at enemies in a Virtua Cop sort of way, which is fun. The graphics and animation on the characters are well-done, and this game has some really nice backgrounds. The bosses suck, though, as it's too hard to see what they're doing on the awful screen.
Duke Nukem 3D - Ew. The images are nice, but the gameplay is horrible. You constantly look ahead of you and lack the ability to turn. All you can do is strafe left and right. So, pretty much, you move forward, strafe left or right to line up with enemies, shoot enemies, move forward to door, and repeat. There are corridors with turns, but when you turn, it's a prerendered animation. Pass.
MK Trilogy - Sloppy. Not much to say here. Two-frame animations, horrible control, nearly impossible to do special moves, and cheap AI.
Arcade Classics - Not as good as people say. Sinistron is almost impossible to play because of the lousy screen. Robotron has some major slow-down despite having a good control scheme. Joust is the most playable of them all, but has control lag.
Fighter's Megamix - They shouldn't have bothered. There are plenty of characters but they all have about 2 special moves, if not less, and the animations don't go past two frames. The hit detection is iffy as hell, too. On the plus side, the images are nicely done.
Sonic Jam - OH MY GOD WHY. It's Sonic with haphazard levels, cheap hits and bugs, TONS of slowdown (everytime you pick up a ring), no backgrounds, and it's in black and white. The horrible Game.com renditions of classic Sonic music will make you cry.
Centipede - Very good game. It's basically a straight-from-arcade conversion of Centipede, with an enhanced Game.com mode. Nothing wrong with this one at all. Good times.
Frogger - Exactly the same as above, but Frogger. Also good times.
RE 2 - I found this one worth playing to the end. They managed to fit almost all of the original game in here. The only difference is movement. You can only move up, down, left, and right, since the game is 2D mimicking 3D. Same goes for the enemies. It works well, though. The only problem is that shooting the enemies requires some lining-up, and there can be some cheap hits.
Jurassic Park - Could have been cool, but fails. Each level starts with a driving scene (think Outrun or something) with dinosaurs chasing you from behind. These are monotonous and poorly done, since they require very basic dodging skills. The actual platform levels have really nice graphics, animation, and backgrounds, but there are a lot of digital sounds for the dinosaurs, all which slow the game down when being played. This hurts the gameplay, because if you're jumping to another platform and a sound plays, the slowdown will actually hinder your jump, and you'll fall and die. This happens a LOT. Not fun.
Lights Out - Lots of fun if you like logic games. No flashy graphics or sounds. Just Lights Out with a touch screen. Yay.
Henry - A sound/picture matching game. Pretty fun and uses the Game.com's digital sound well. The AI is pretty sad, but you'll have fun playing just listening to the stupid sounds.
Wheel of Fortune - It's Wheel of Fortune. You'll either like playing it or hate it.