Repo now has Fo2 style merchant inventories. That means item distribution is random (based on vanilla inventory of course), but at the same time their inventory will refresh every few days. This, too, can be disabled in fo1_settings.ini of course (can't be disabled in an already running game if the merchant / map has been visited already!)
Personally I find this way more exciting, as you can't rely on your default merchant trip anymore. Also I've added a few special weapons with low spawn chance to them, so if the god of random wills it, you can aquire some fancy stuff.
Can't say anything about party member perks right now, as I haven't started reworking their scripts yet.
Special encounters all have a 1% chance, and have a min player level requirement. I've added this because they happened way, way too frequent in my tests (even with low luck). Hell, I know it's a bit of a cult thing happening, but I got the alien blaster right after leaving Vault 13 in at least 3 different playthroughs. That's just overkill.
Mysterious stranger is not a super mutant. You sure you got the latest proto files and have set them to read only?
Are You saying i need to manually apply read only parameter to proto files *every* time i do an svn update?