well for one the GBA version is smaller, i.e. the blocks are sized down to fit into the screen. You can actually play the game sideways to make the blocks appear proper, but it's more pain than it's worth.
I have only played Pokemon league with friends, and I always choose Misty coz she has staryu or starmi (HAYA~!!!) so I do not know about the kind of modes the game offers, or about its options.
but in comparison to SNES tetris attack, one noticeable difference was in the timed 2 minute mode, you play with only 5 color panels instead of 6.
That may affect your score depending on your skill as a player.
I also don't kno how the scoring has changed. I believe Pokemon league fixed a scoring issue that was in TA/PDP which dealt with chains reaching over 14. Unless they tweaked the scoring even more (like in the Gamecube puzzle collection), I would assume this game scores the same as Pokemon League.
o yeah, and there isnt any 3D mode in GBA version.