About Mutant Invasions: Pretty sure the sliders were still in-game. Necropolis had it, so did The Hub and Followers. Hub and Followers were bugged and always showed up, no matter what you did. My memory might be fooling me, but I'm pretty sure Shady Sands had a mutant invasion ending slide. Shady I am sure, Junktown I am not. The Brotherhood was supposed to feature one, but it was removed, it was supposed to be part of a quest where you find a spy there, and if you never found the spy, the Mutants take it over.
Further thoughts about Mutant invasions: Yeah there were three timers. Water Chip Timer, Vault Invasion Timer and Mutant Invasion Timers for the cities. Necropolis was the only one which actually kept the actual mutant invasion in-game. AFAIK, you could stop the Necropolis invasion, I think you had to destroy the Military Base before the date of the invasion, or destroy it and then visit Necropolis. I think Set actually gives you a reward for doing that. That, or killing The Master. Either one, someone correct me.
Vault Invasion Timer was also decreased if you sent the caravan to Vault 13. So yeah, by increasing the timer for the first quest, you decreased the timer of the second one. That was actually very clever. I don't remember what it did after the patch which removed the Vault Invasion Timer, I think it actually brought it back.
Honestly, I thought the problem of Mutant Invasions is that they are a bad timer. You have abso-fucking-lutely no idea this Timer and Mutant Invasions are a thing, unless you run into Necropolis invasion, but that was a bad timer by itself. Its pretty much meta-gaming.
If you asked me how it would better re-done, I would make it so that the Mutant Invasions timer only kick in after the Water Chip quest ends. This is because, according to that ghoul guy hiding behind a bookshelf after Necropolis invasion, the Super Mutants are after You, The Vault Dweller. Further, I would engineer a way to make it so that the player can know that timer in-game somehow. Say, intercepting mutant transmissions using that radio carried by the dead mutant of the Missing Caravans quest (I can't believe I remember this guy carries one). Furthermore, I would make it so that its possible to speed up or delay the mutant invasion timers. We know you can speed up the Vault Invasion by using the services of the Children, and using the Water Caravan for Vault 13.
(I would also make the Super Mutants in general far more powerful, they're pretty wimpy without Plasma Rifles if you ask me. Heck, correcting the ridiculous laser resistances would make them a lot more badass, because while Gat Lasers are harmless at 90% Laser RES, they would be a total terror at lower levels of resistances. This would also make The Master a lot more credible and dangerous as a Final Boss).
Hmmmmm... I wonder if increasing Super Mutant and Nightkin Numbers would work as a way to represent the results of the invasions in-game? So encounters with Super Mutant/Nightkin patrols get harder and harder, and Mariposa and the Cathedral get more mutants/nightkin. If a city is invaded, the Encounter Table gets replaced with mutant encounters, floaters and centaurs, and maybe keeping the odd raiders/gang and monster encounters.
Cities are getting destroyed left and right, and your enemies keep increasing in numbers and appearing everywhere. I think that could make the end-game pretty frenetic, if done right.
Btw I find it kinda funny that while the Followers have an ending, Boneyard itself (or Adytum) has none. So to date we have no idea what happened there. Did Vault Dweller do the Regulators' dirty job and murdered the Blades? Did the Blades go in by themselves and shot the Regulators up? Did the Vault Dweller help the Blades and joined in their attack? Did the Vault Dweller deliver the tape to Zimmerman and then destroyed the Regulators themselves? Did the status quo keep up? Was Adytum invaded by Mutants?
No one knows, no one even has any idea, not even in New Vegas there was a peep about what happened to Adytum. About all we know is that the bugged "Followers survive" ending is canon, the Gun Runners moved from Boneyard and that's it. Not a peep about Adytum.