In my opinion, I think it would be preferrable to give the Hero of Time a break for a game such as this, but if Link were be in a game revolving around Ganondorf's vengeance, I'd give him a recurring role like King Bulbin in
TP, possibly as a boss, maybe even of final boss.
If Link were to be in it, it would also be cool if Vaati came into play and Link and Ganon had to put their differences aside to team up and defeat him, only to have a sequel for the two to resolve their relationship as rivals. I know, I've put quite a bit of thought into this.