I generally refuse to put things on a clear hierarchy as any story has pros and cons and alot comes down to personal preferences. Though for me I didn't read / played that many AVNs, in my favourite pool are besides Cosy Cafe: Ripples, Harem Hotel, Lucky Paradox and The Headmaster. For each I have very different reasons.
Though , after playing all of them, I followed a suggestion that I heard countless times and finally tried Eternum. I have to say I don't want to put down any other AVN, but Eternum is quite literally on another level. Most impressive to me was the excelent choice and amount of music besides the incredible concept which combines movies like Ready Player One, Matrix and a few other genres.
Note that I don't want to say Eternum is somehow "better". Each AVN has its own style and elements which often can't be compared. The nice thing about Cosy Cafe is, that it uses a much more realistic setting. No crazy superpowers of scify elements. It focuses much more on down to earth problems and interactions. To me the lack of choice makes a much better coherent story and you can actually enjoy all the content that fits perfectly together in a single story. Having too many branches in the story will just shorten the story and often creates some inconsistencies. I read somewhere the Cosy Cafe was originally planned as a cafe simulator with a similar week / day cycle as others like Haram Hotel or Lucky Paradox. I think dropping this for a linear story is one of the biggest factors which made the story that great.
Finally one of my first AVN is a (of course now abandoned) story that as a lot less lewd content but an actual story. It's called CobraVenom which is a crime / special agent setting where your partner got killed on a secret mission and you take care of his family. It's a lot more about relationship building and the actual story about the double life. It hasn't quite the quality as others. The original language is russian and in some parts the english translation could have been better, but I thought the story was great. It seems the developer just disappeared after the Ukraine stuff.
Ps: An honorable mention has to be "that new teacher". Even though the story and especially the girls behaviour is way over the top, the humor is actually great and I think the idea of having guest characters of other AVNs built into the story was a phantastic idea. You actually get some tangential interaction with Lucy from Cosy Cafe, but many others from other AVNs, like Stormside (which unfortunately is also abandoned). I would like to see such well integrated cross-promotion between AVNs more often.