In general I'd rather see the game industry start developing more spin offs or new IPs to increase character diversity rather than gender-bending existing characters. Link is is an interesting case since most Links are reincarnations of one another, so a gender swap isn't impossible, but if most other IPs it would be totally unjustifiable. That said, just because Link could female doesn't mean he should be. Nintendo could easily put Zelda in the lead for once, her Sheik alter ego proves she can kick ass and in Hyrule Warriors, the spin off, she showed she can kick ass without dressing up as a boy as well.
To directly answer the question though? Case by case basis. Basically if a character I really liked was gender swapped I probably would not buy the game. If a character I didn't give a shit about was gender swapped I would either be no more or less likely, or slightly more likely if it was male to female. This is due to me having a strong preference for female playable characters. That said I have a hard time coming up with games where I would buy a sequel I wouldn't otherwise buy if they gender swapped the main character. It's so much easier to just use a new character, or catapult a supporting character to the main role.