The idea is to make the game as enjoyable as possible

Enjoyable to whom? There are players who like linear games, players who like sandbox games, and players like me who don't care one way or the other as long as the level of openness contributes to the game as a whole. When designing a game, every decision removes possibilities; the final product is the one you leave behind.

W.r.t. catering to "I just want to play, not be bothered by the main quest" players, I think the main thing is just to ensure that ignoring the major quest-lines doesn't hinder progression in other areas. Say, in game A, the reward for completing main quest milestones is the unlocking of new continents, the availability of new crafting materials, new spells, new party characters, and experience points. In game B, the only main quest rewards are new party characters and experience points. If you want to cater to the "anti-mainers", then tend towards game B, so that they can pursue their own quest (say, become the greatest blacksmith) without ever having to say "Damn, I need some obsidian, and it's only on the other continent; I guess I have to go fetch six dragon eggs for that idiot king after all."

I'd put myself in the "anti-mainer" camp, actually. Not because I don't like stories, just because at this point I'm tired of "fantasy main quest" stories. I wouldn't say there's a ratio I'm looking for, though. It's more a structural question, of whether I can genuinely pursue my own "quest" independently of the main quest.

Actually, what I really want isn't sidequests, but progression that isn't tied to a quest structure at all. While playing Skyrim, one of the things that took the depth out of the world for me is that there were few details that weren't eventually part of your big list of quests. I kind of wished for... to use a school metaphor, "self-study" rather than "taking courses". I might have liked learning the "shout language", or collecting the singing plants, or doing "archaeology", except that in each case I couldn't quite feel like it was *my* goal. It all feels like it's just there to support some quest... and there's a feeling that if I'm not on that quest, I shouldn't do *anything* lest I mess up a future quest and not get fully rewarded. (Like, I shouldn't kill that particular monster, because killing it is almost certainly a future quest, because there's little non-quest-related material in the game, and so if I kill it too early I might miss out on an important reward.) In other words, making activities into formal quests and adding external rewards to them can lead to perverse incentives, inhibiting the player from pursuing that activity unless specifically instructed to.

See I have thought about the problem of finding things or killing monsters too soon. I think the easy way to do it is to have a quest item for the monster kills and just have the area marked on the map.

If a player discovers something before they are meant to, I don't want them feeling penalized. I also would make certain quest items removable from your inventory or have a separate inventory for quest items, perhaps even using quest completion to add more space.

Yeah, being reasonable about quest fulfillment mitigates a lot of those problems. It's not really quests that are the culprit, it's complicated and arbitrary quest flags and the possibility of accidentally making the world such that the quest flags can't be flipped. And yeah, I don't think it requires being super-clever about quest flags. Being "dumb" is better than being smart, I think: having quest success being defined solely by end state ("Giant spider is dead", "Goodman Smyth has a dragon tooth in his possession") rather than making quest success depend on certain events happening in an expected order.

I really like a perfectly balanced, 50-50 ratio, kind of like Golden Sun, where you could play the plot, or save Ivan's master, or collect Djinn.

Along those lines, I thought Legend of Mana had an interesting structure. There were nothing but side-quests, but three different chains of them could lead you to the end of the game. If you ended up not liking the plot or characters of one quest, nothing prevented you from pursuing the others. (Not that you know this -- you don't know in advance which quests are going to lead to the endgame. You just pursue the plots that you find interesting.)

As quests, they were often the epitome of "JRPG-arbitrary", consisting of wandering around trying to figure out what arbitrary actions would start the next critical cutscene. So it's not the quests themselves that caught me, it was that I felt like I got to choose which quest arc was the "main" one and which arcs were optional.