Coming from a strictly collecting standpoint, I'd say it's very subjective. If I'm collecting games from a series that goes multiplatform I'll generally gravitate towards the system that has the most games in that series for it, since system-exclusive games do still happen every now and then. However, even though there were 5 Mega Man games on the PS2 compared to 4 on the GameCube, I broke up my purchase decisions based on in-game content. I went for Mega Man X Command Mission on the GameCube over the PS2 due to the GBA functionality in the treasure radar (despite the save data cross-compatibility with MMX8, a PS2 exclusive). I also initially bought the GameCube version of Mega Man Anniversary Collection because of the video interview with Inafune on-disc. (I later sold all copies of both the Classic and the X Collections because I already own the originals and, speaking as a Mega Man fan, the Collections are total garbage no matter what system they're on.)
Just in case my rambling didn't help, here's the run-down on what I think in your case: I would recommend that, except in the case of system-exclusive games, you prioritize collecting for the system you like best. In the case of true non-preference, go with the version of the game with more appealing features (if there are any differences between them). In case all versions of the game are otherwise identical, either flip a coin, go with the most comfortable controller, or get whichever version is cheapest and/or most readily available with little hassle.