this kinda surprised me too, but the download play of ADvance Wars one was pretty crappy - a small map, with set deployed units.
The link mode has few gameplay advantages over hotseat (AW1): During fog of War, you can see units trundle through your range of vision, and you can see the battles happening (if I recall correctly - and this only really matters if you are playing against sonja, and you want to see how much damage is done? - can't remember if you can see the health of units during battle).
Hotseat has advantages of setup - players don't get bored, you can play other stuff while passing a game around, or have multiple games going at once (did anyone ever do this?).
Personally, I like the link, because I'm ultra possessive, and I don't want people touching my GB (it's kinda fun huddled up with your own unit). They need to allow you to do something while it's not your turn, say, examine the units and map, or allow some kind of pictochat with other nonactive players (haha for making alliances, and telling other people what you can see).