While that's all very true, for me it's about the presentation. I feel like that stuff worked in its own context with the primitive visuals, or when you're younger it doesn't seem so bad. When you're playing an epic, kinda over the top videogame back in the 90's it doesn't really matter what goes down. When you watch a 90 minute CG movie at an older age, the stupidity is unbearable.
If they took those scenes from those games that you pointed out, and put them in CG movie form, they would also be terrible. It's also in the art direction. In older games, silly stuff usually gets a pass, but the more "realistic" it gets, the harder audiences are on the silly stuff-- because they're trying to mix more realistic visuals with stupid scenarios and IMO it makes the awful a lot more noticeable.
What works in videogames rarely translates well into a feature film. It's not just when they try to do it live action either. If some studio re-created Super Metroid into a 90 minute CG movie with "realistic" art direction, it would probably also be terrible.
btw, Kefka's line is great. Rarely do villains actually have some sass, especially compared to super serious villains these days like Caius.