I'll be honest, despite Gen III being my least favorite, I would still like to see it remade with the modern graphics.
I was surprised that Blaziken was really given a huge boost when Gen V came around with the Speed Boost ability.
That and Gen III's legendaries are its saving graces for me. Swampert seems like a Gen III Quagsire, and Sceptile doesn't have the status moves to be an effective staller.
They pulled out all the stops for Gen III's legendaries, though-Groudon, Kyogre, Rayquaza, and the Latis are my favorites. As previously stated, Latios more than the others.
I could have lived without the Regis, though.