1. Fillers and Dragging storyline - Unnecesary scenes that just have nothing to do with anything at all can ruin a good storyline. It makes the development of the story slow, making it a bit boring. Though I don't think I can find much VNs with no fillers at all (fillers actually help the reader became attached to the characters), it would be good if they can be minimized. Also, some stories just develop way too slowly, which makes it similarly uninteresting.
2. Rape, NTR and BDSM - I think I would never be a fan of rape, ntr or any BDSM play for H scenes. Call me naive, but I think sex is an act of love and should not be forced upon onto the other.
3. Overly attached Imouto (or Imouto-like) Heroines- I actually like some imouto-like heroines (like Yume of DC II), but I just hate it if the imouto is overly attached to the protagonist. It makes me see them as some spoiled brat.