The 3D background planes surely will make their way into the game, same as the background transparency effects (clouds and other stuff), since the GBA can pull off those effects in a very similar way the Saturn does (and it's much close to the way the SNES does those effects as well).
But the polygonal bosses.... hmm... maybe. After seeing Crazy Taxi, I think they might be in there, toned down, of course (the lower resolution allows Treasure to cut off detail without people noticing it).
The GBA has a speedy processor, so I think it'll hand almost the same amount of sprites without extra slowdowns (the saturn itself would slow to a crawl if you keep using the lock-on weapon). Of course, the sprites will have to be scaled down, otherwise they'd be too big on the screen, leaving little space for navigation.
I'm also confident the game will have some differences, mostly in level design. Not for better, not for worse, but, different, thus making it a fresh ride for anyone who already played the Saturn version to DEATH.
Did anyone here played the GameGear version of Gunstar Heroes? It's easily the most impressive GG game I ever seen, and the gameplay is as tight as the Genesis version. The levels are the same, but you'll see they are different at some points (hardware limitations forced Treasure to redesign some areas), like the mining car level and the shuttle level, and some of the latter levels. The game is then, as fun to play as the original, but if you already played the original, you'll find new touches that freshen it up.
Oh, and Seven Force is in there, almost INTACT.