One of the really good benefits of having multiple characters at end-game is that you make twice the amount of weekly tomes per week (since you get 450 on one character, and 450 on the other). If you play it well, you can gear up a different job on each character simultaneously (ie, I gear DRG on my main and AST on my alt). Having two level 80 characters at end game is a lot of work, especially getting the secondary character there in the first place, but for my own purposes it was very worth it.

As for adding rewards for having two characters and doing various feats... idk. My only worry about that is that it'd become very pay to win (depends heavily on the achievements) because the mogstation sells both story skips and level boosts, which would cut out 90% of the work.