Probably many of them are subjective.
In the case of Yoshi's Island, I suppose many would say GBA because it has a few extra levels.
But Yoshi's floating sound effect is to me a sound replacement that is almost as annoying as Mario's crying. Also I'm not sure if the game really took the lower resolution into consideration in the port. (1-E is the level that made me wonder that, the part where Yoshi has to dodge a mace while landing on Poohie while the screen scrolls down rather unfair, like it's still meant for the SNES' taller vertical resolution which allows for more reaction time)
I'm sure SMW and probably SMB3 did make some level adjustments to account for the resolution difference.
Tales of Phantasia, I'm not as familiar with but I hear it added some PS content, like an extra player character. But as usual, lower sound quality and some slowdown (never mind debates about the localization itself).
Aero the Acrobat added a save feature to the game (which might be a godsend for some, considering many considered the original an unforgiving game) but in a few minutes playing it, I recall the controls were more slippery than the original (I remember people complaining about the control in the original, but I don't know what was so bad about it. Maybe the unusual "drill attack" mechanic takes a bit of getting used to?)
Breath of Fire 1 and 2 I think used translations mostly copy-pasted from the originals (a shame as even in 2002 people had told Capcom well what they thought of the original BoF2 translation). But they added quicksaves as well as, at least in BoF2, an EXP/zenny boost to speed up the game. I only played BoF2 as far as Highfort. Seems the game has a tendency to crash at the cutscene after finishing it, maybe igniting some PTSD from those who remember getting trolled by that dungeon in the original.
R-Type III is apparently a unanimous "original". Sounds like there's many reasons that (last I checked) the SNES version was ballooning in price while the GBA version remained cheap.
Also, a couple Japanese RPGs missing from that list, but probably few people played them for that reason.
Metal Max 2 Kai (Data East released that game on their deathbed, shelving the MM Returns port as a result)
Sansara Naaga 1x2
Super Chinese World (Ninja Boy) I think got a two-game compilation as well.
I hear DKC3 got a different soundtrack on the GBA, not sure if it's enough to make it a recommendation though.