1) Players grow more attached to 1 character when they level multiple jobs on one.
-> This way they stay longer in the game so +1 for the company and for the players.
2) Your proposed system won't work out since people will just make multiple characters.
-> As a player, I won't know who the heck your alternates are. I won't even care who the heck you are. You think I would go track all "x" number of your alternates multiplied by "y" number of players in my linkshell? It seriously sucks bad when I log into the game to ask "Who are you" every day.
3) Flexibility in groups.
-> Granted there are some balancing issues but anyone can theoretically go as anything in groups...and I don't have to re-log a character to do it.
4) Cross-class skills
-> I actually liked this aspect of FFXIV. Even if everyone uses the same thing in the end, it is something unique to FF.