These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Ensemble Dark Horse: A case could be made for Agent 12 who, despite having a fairly minor role that could have been covered by Belthasar himself, has garnered a pretty decent fan following if the comments on the YouTube videos are any indication.
Game Breaker: Due to a massive overhaul/upgrade in new techs for most of the characters, Glenn and Ayla find themselves in this territory. Considering the game never got past the 98% beta, it's very possible that these characters' Game Breaker traits would have been Nerfed somewhat before final release.
Misaimed Fandom: The quote at the top is thrown around quite a bit on the videos and amongst fans, as well as a lot of Zeal worship in the game itself. Very "ZEAL SHALL RISE AGAIN". It's as if they don't realize there were many reasonsfor thekingdom's fall.
Just because Queen Zeal has been corrupted by Lavos by the time Crono and company arrive doesn't mean every ruler in the entire history of the kingdom was like that. It even seems like the kingdom was an actual Utopia before Lavos/Zeal messed everything up.
..Except for the whole exiling-all-non-magic-users-to-the-frozen-wasteland-beneath-the-clouds thing. I'm pretty sure Zeal was meant to be seen as an exercise in hubris from the very beginning. The queen's attempts to control Lavos were just the final nail in the coffin.
More than these fights, it's the conveyor belt puzzle in the same section that's really annoying. Also, the frog hunting minigame in prehistory: due to bad coding (both the unpolished state of the beta and over-ambition from the developers, probably), makes the capture of a few frogs an exercise in frustration. Luckily you need just five to succeed.
Tear Jerker: The Fall of Guardia and Schala's fate. And, finding Marle's corpse.
Marle and Lucca's Flame Trials.
The video of one of the Developer's Rooms, where the various developers talk about their excitement for the game, how much they were looking forward to it coming out, how all the hard work was worth it, and thanking Square-Enix for making two great games for them to work from... Ouch.
That One Boss: The Vision Serpent can be a real pain without level grinding.