That is a fair point, about the extra content (although it did excist as DLC as well if i'm not mistaken). The reprint of AE did nearly 110k, which is pretty good as well.
Maybe MGS has a small edge, but from the sales data i've seen, i dont think that i would concider MGS or RE as being a noticeably bigger franchise than the other.
I think the main difference is that when we're talking about Japan, RE used to be a multi-million selling franchise which eventually dwindled to the 600k+ franchise it is today. MGS on the other hand was always a 700-800k franchise in Japan, and remains as such to this day. So I would say that MGS has retained its popularity pretty well, while RE has not.
Famitsu numbers:
Metal Gear Solid - 705,736
Metal Gear Solid 2 - 798,185
Metal Gear Solid 3 - 819,807
Metal Gear Solid 4 - 706,461
Metal Gear Solid Peace Walker - 791,577
Resident Evil - 1,194,779
Resident Evil 2 - 2,154,975
Resident Evil 3 - 1,383,282
Resident Evil Code Veronica - 403,962 (DC) + 338,307 (PS2)
Resident Evil 4 - 220,799 (GC) + 454,979 (PS2)
Resident Evil 5 - 520,564 (PS3) + 123,817 (360)