They seem to have expected some things, though, see adding pets with aquatic damage (gun and ooze) aswell as a resistant cockroach to stop us from cheesing everything with elementals. Yet, a fact their damage output is low combined with shields not checking for racial damage means this mechanic prevents a lot as you mentioned. The last boss has got an ability to remove basic shields so perhaps that was not in oblivion either… unlike the reactive damage. Also, an ability that forces swap altogether with an ability which prevents from being swapped, including critters? I can't say I like it.
At some point, Zygor was destroyed. Accounts differed as to what the cause of this was and when it happened. According to one account, the planet was destroyed in the war against the Xaranti. (PROSE: The Bodysnatchers) Another account given by the Zygon Broton in the 20th century said his world was destroyed in a "recent catastrophe". (TV: Terror of the Zygons) Another account, given by Elizabeth I who had been posing as a Zygon in 1562, said that the Zygons lost their world when it burned in the first days of the Time War. (TV: The Day of the Doctor) 

Occasionally it's also been proposed to re-randomize all the gear. We didn't have best in slot lists back then. People weren't starting out as a fresh level 1 character with a complete list of which dungeons to run at 60 in order to gear as quickly and efficiently as possible. Now, all that data is available. If gear were re-randomized then all of those lists would become useless and thing would be close to how they were. Which is a more important part of the "vanilla experience?" the fact that item X from boss Y has exactly Z stats on it, or the voyage of discovery? Personally I think that voyage is way more important. Do you remember how many points of which stat on the ring or whatever that Darkmaster Gandling drops? I don't. Would it kill your experience if the BiS for every class were in a different dungeon so people had to actually play to figure it out rather than simply consult a spreadsheet? I don't think it would. For that matter, it probably wouldn't be a bad idea to handle it intelligently so that the better gear is in later dungeons. I remember there because some weird cases where level 40ish gear was better than anything that dropped in level 60 dungeons.
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