Combat is turn-based and there is no time limit on each round in a PVE Pet Battle. You can take your time to determine which spell to use next. Some pet abilities have multiple round cooldowns, while others can do extra damage if certain conditions are met. Be creative and have fun testing which combination of attacks works best against different wild pets!
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.
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.