I know what you mean, though our reasons might not be exactly the same. I was put off mostly I think by a combination of the awful graphics (faction member portraits excluded) and complicated interface (too many long menus) and just the overall feel of the gameplay.
For years, off and on, the good reviews kept me coming back to AC looking for another in-depth turn based strategy experience. But I could never get into it, meaning that I didn't play for more than fifteen minutes before deciding that it was too complicated/unplayable.
Well recently I decided to just give it a go and make an effort at building a expansive empire just like in Civ to see where things go. A few hours later I realised I was hooked.
For me it's a good compromise between Civ 2 and Civ 3 in that it has some of the newer features of the latter, like automated workers (I really recommend setting your formers to auto if you don't already, unless you're really into the micromanagement, it frees you to focus on other more pressing matters) and well defined borders, but retains some of the traditional elements of the former. I always hated that they got rid of the diplomat unit in Civ 3 so it's a pleasure to use AC's probe team. And I think AC's government options are far superior to both Civs, it gives you more control and has a play in your relations with other factions. Although overall I still prefer Civ's more familiar unit types and tech tree, AC will do me well until the release of Civ IV and I'm glad I had a chance to fully experience it before it's too outdated.