Pretty sure some of this stuff is probably stated in someone's post above here, or you just know this stuff, but here's what I think a good VN needs to have, though these are also blended with some personal stuff as you'll probably tell:
1) An MC that develops- I'm not a big fan of MCs that are either stupid/dense as all get-out unless girls literally throw their naked bodies towards him, nor am I a massive fan of MCs who are overpowered as hell unless the sex scenes are good. Personally, I think a good example of this would by the main character of the Maji de Watashi Ni Koi Shinasai! series, Naoe Yamato. Personal favoritism towards this VN aside, the best example of this comes from A-1's route with Azumi, where he needs to learn to be an effective butler amidst the sea of superhumans that work right next to him. TL;DR, don't have a strong MC, have an interesting MC. Even if they have a superpower of some sort, make them learn and develop it. But that's just me.
2) Great writing, especially during any steamy sequences- Although I love F/SN, the visual novel's sex dialogue is a bit strange sometimes, at least IMO. But in general, as long as the dialogue sounds like a natural conversation, you don't really need to worry about something like this.
3) Choices that matter- I personally don't mind bad endings. What I do mind, though, are choice that don't really make a difference. It makes me wonder, "If me save-scumming and retrying the choice doesn't make a difference, why have it there at all?"
But again, these are obviously tainted with personal ideals, so take them with a grain of salt unless you already understand them. Then, go about your business.