I don't think there are much of any, at this point. There aren't any game-breaking ones, at least (ala Vault 11 security turning House against you, etc.) As I've played it recently there are a couple of broken flags, such as Mr. New Vegas reporting that you failed to take back NCRCF if you aided the NCR siege, or a particular ending slide for the Followers bugging itself out of existence, or the coding error that gives you 200 karma for killing "mild" evil characters like ghouls and fiends and 2 karma for killing the only "super evil" characters (Cook Cook and Vulpes Incata). At this point I guess the House-BoS truce is cut content that needs to be restored via modding.
Bergman's announcement only really covered gun tweaks, because there are a lot of weapon geeks out there, and JE Sawyer is one of them. I wouldn't be surprised if he tested and coded all those tweaks himself.