You're all dense. Games are eliminated because of difficulty obtaining them. Ease of acquisition is a determining factor in candidacy, but it is not part of the mission statement.
I don't think Mother 3 is a great candidate personally, not because everyone playing it will be using pirated copies. It is a concern. However Jonathan makes the candidate lists so in the end that is his discretion.
I think its a bad candidate because this is the GBA retrospective, and there is nothing "retrospective" about a game that was released postmortem and in reality was never released at all. There are other, more important, games in the GBA library. However, that is my personal opinion. It extends to games like Mario Tennis, which is really only famous because of an absurd review.
Honestly, I'd rather we dictate from on high the games we're going to do. However, we don't.
There. That's as official as you're going to get regarding the goals of Retroactive.