A lot of the problems I had with BG2 had more to do with specific design choices than with the overall style of the game. Avoiding (or ignoring) the problems I had with it while still having a similar style of game is pretty easy, IMO. Taking the specific things I listed a long time ago:
* CNPCs - Many of their introductions didn't sit well with me and I felt that there were too many who didn't have an equal amount of development given to them. While it was great that so many of them had a ton of quest content, I would have preferred a smaller list of companions with more attention to each one. This is what we said we were going to do at the start of the Kickstarter and it's what we're still planning to do.
* Being required to find/save Imoen - I didn't like it then and I still don't. I wouldn't make the player rescue an NPC with whom he or she may or may not have a positive relationship. It's a very specific plot point and easy to not do. I understand that a lot of people have no problem with the rescue plot, which is totally fine, but I don't think that particular plot point needs to be repeated in PE.
* Style of dialogue - I prefer naturalistic -- some would say "dry" -- dialogue. BG2's characters are much more expressive. This is a personal thing and I recognize that most players *don't* like the same style of dialogue that I do. What I strictly prefer and what I write and have others write are not the same thing. My characters in F:NV are still on the dry end of the spectrum (e.g. Arcade Gannon, Chief Hanlon, Joshua Graham), but there are plenty of more flamboyant, expressive characters in the game that other writers developed.
* Being flooded with quests in Athkatla - To be honest, I don't think is a controversial opinion! I've seen many other players say the same thing. BG2 has a crazy amount of quests, which is great, but the density in Athkatla was a little too crazy. I think those quests should have been spread out or staggered in some other way. PE is going to have more of an exploration focus than BG2 (though not as much as BG), so I believe that will help spread the content out more.
Even though I had those problems with BG2, my job as a lead designer and project director is not to create content that appeals specifically to my tastes. Obviously I would have a difficult time making a game that I *disliked*, but I have (and continue to) push for elements I feel that players will ultimately enjoy even if I'm not super thrilled about it. That's my job.