Well, only cause you asked
I wouldn’t be a good person to ask for what to include, for many reasons. I’ll list them for you:
1 – I like otome (so things like Hakuoki would be on there)
2 – I like gameplay VNs (so things like LittleWitch Romanesque for its excellent sim gameplay.)
3 – I like OELVN's, mostly because of the above two points (so stuff like Scheherazade would be on there. Then I'd try and push the boundaries to include Academagia, even though it's an interactive fiction/sim hybrid and not a visual novel/sim hybrid )
4 – I like things to be logically consistent, so I’d either take a very narrow view of what a VN is and be consistent with that (which would generate complaints, as I think yours did when you didn't include gameplay?) or I’d take in a very wide view of what a VN is (which would mean Phoenix Wright will be on there…) I find your list to be a little inconsistent but I'll get to that in a minute.
As you can see, my suggestions wouldn't be good suggestions for your list.
My disagreements with your list:
Well, you say you’re judging things on story only but you included Sengoku Rance. As a fan of Sengoku Rance I can tell you that almost all of the appeal of that game is its solid turn-based-strategy gameplay… and the sex scenes. In fact, I'd categorise it as a strategy game first, and a VN second. If you include Rance I'd ask why you haven't included Kamidori. Both don't have very good stories but are well received mainly because of the gameplay.
Daibanchou – see above.
You have things on there like Dangan Ronpa and 999 but not Phoenix Wright. I understand you’re probably using VNDB’s definitions, but they’re dreadfully inconsistent, which is part of the reason Fuwa should provide its own, liberal definitions. Phoenix Wright deserves a spot if Dangan Ronpa is on there imo.
Speaking of which, I found 999 to be dreadfully overrated also. It has a bloated and repetitive storytelling style which didn’t appeal to me. WinkBlinkel kept trying to shove it down my throat cause I kept trying to shove Divinity: Original Sin down his throat. Neither of us were successful.
The next two points are VERY opinion based:
I hate Kira Kira with a passion because of the level of boredom it produced in me. The level was more than any human could bear…
I think Dysfunctional Systems is grossly overrated. The art is nice but, once again, not a fan of the prose.
But at the end of the day this is your list and I wouldn't worry that I disagree with it. You've read a lot more VNs then I have, and overall it's quite a solid list of good introductory VNs. Your taste just isn't compatible with my tastes (I don't like dark or gross stuff, so I won't be touching Saya no Uta with a 10 foot pole, for example.)