What I meant about WoA was that it did not provide answers to many setting situations. It explained the Deepness--which I was thankful for--but what I wanted was answers, not more questions. Of course, once I read HoA, I was thankful for WoA more (because the questions it posed were the perfect setup for HoA). However, I still liked WoA the least, because it lagged in the center there. I can only attribute a lot of this lag to Zane. In fact, I don't even like the name "Zane". Everything about him made me... not care.
Elend, on the other hand, is my favorite character throughout the trilogy. His character arc was handled very well in WoA. Well of Ascension is still a good book, I don't want to sound like I'm belittling it. I just thought... well, it's all Zane's fault I didn't like the book as much.
That being said, once I do a reread of the entire trilogy, I may change my mind, but I think it's unlikely. Final Empire is #1, Hero of Ages a close #2, and then Well of Ascension easily #3. I don't think that any amount of rereads will change that, because I remember my pure visceral reaction to finishing each book. Final Empire was the most powerful to me.