ahwawawa... this is rough. I can eliminate some choices right out, still haven't played My Girlfriend is the president, and I couldn't get into either Saya or Hoshizora. Clannad, I did enjoy, but it had some really bad moments, and I don't think it will stack up against the other powerhouses in this poll. Uta was fun, and I quite enjoyed it, but the end was pretty horrible.
So I think in the end, my problem comes down to three VNs I love to death. F/SN, Katawa, and MLA.
Fate was one of the most epic things I've ever experienced. And I love Rin to pieces. However, the adult content felt a bit forced, and the CG art in the h-scenes were lacklustre to me. The story was amazing, and I played every last route, and just sat there overwhelmed after finally seeing the true end.
Katawa was also a great experience. I'm not into slice of life much, but I just couldn't get away from this game. I played through every last route, and loved it. Lilly warms my heart as a character, and she will always be special to me. If I had to think of negatives, It had a few moments that didn't click as well as I might have liked, and there was little to no fantasy or difference from real life.
MLA is the most recent VN that I've read, and it was amazing. I appreciate Sumika, but I'm actually more fond of a couple of the other girls in the game. The h-scenes didn't impress me at all, but the lore blew me out of the water with the depth of the world. Little details and technology were both great, and very slow to take it all in bordering on boredom during some in game lectures. There were so many epic moments, from shock, and combat without really having control over it in a game like situation, and there were the small little animations like blinking eyes, moving mouths, and the cold breath that I've still yet to see in other games.
Ugh a tough choice... I think I have to be honest, and as much as I love Katawa, it seems like it dosen't compare on the plot level of the other two, so I will eliminate it and decide between Fate and Muv-Luv.
I think in the end I was more frustrated with MLA than I was FSN, and MLA effected my emotions quite a bit more than FSN. So while both are really great, I think I have to go with MLA. The plot and lore really pushed me over. The story being FSN was great, and interesting, but it was based more on an almost shounen concept of battle, while MLA had this really great time travel/dimension jumping/harsh as well sci-fi world that you could feel through to your pores.
So yes, after all this, MLA gets my vote.