again, what retconning?
(SPOILER)Big Boss being alive
Liquid being dead the whole time
Mei Ling having a different accent
The data on the Patriots retrieved from GW being a load of rubbish
GW was destroyed but then got repaired
The Patriots aren't humans at all
Naomi has cancer
Metal Gear REX, after you literally blew it to pieces in MGS1, manages to get back operational after fiddling with the power for a few minutes
Snake's Foxdie now has the ability to kill everyone on the planet

The game was still awesome, just some of the things were fine as they were and didn't need to be changed.