Different qualities aren't limited only to wild pets—many rare World drops and special non-wild companions have had their stats boosted. For example, the world-drop dragon whelps (Azure Whelpling, Crimson Whelpling, Dark Whelpling, and Emerald Whelpling) are of [rare] quality. Check your Pet Journal to see the color-coded rarity of your non-wild pets.
Most people who have spent years playing massively multiplayer online games will tell you that there's something special about the first one you played, too—and WoW was the first for many people. You can become so swept up in the uniqueness of your first experience that you overlook many flaws. It's likely many look at WoW Classic with rose-colored glasses, just as many simply forgot which features were added when. And some of today's WoW players may be too young to have even played vanilla WoW as it once was.
Only really to expand on Gráinne's comment as regards the 'collecting' and 'roster development' sections - which are, as said 'distinct' although they are intrinsically linked - I would like to point you in the direction of the in-game Achievements > Battle Pets > Collect tab. There are a series of achievements called Raiding With Leashes, pretty much all of which can be completed via the auction house - if you have the gold/inclination - or by completing old raids.
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.