ChesHatter: At first, I wasn't too crazy about what little carried over, but I've grown accustomed to it and just accept it now, which has lead to more enjoyment from the game.
Fenixp: Honestly, I feel like it goes very well with the nature of the game which is very similar to a board game (if you played any cooperative story-focused board-game, you'll know what I'm talking about. If not, your life is robbed of great experiences.) The starting conditions are only ever changed by the decision of the player, not by progress or unlocks. I'm okay with that. The card mechanics added by the expansion are rather interesting in this respect and I still can't decide whether I like them or not - but it's nice to see that even unlocking those is presented in a form of gaining booster packs.
I feel similarly about the cards. I enjoy that they bring a little mix to the game (and I finally had something that carries over ;) ) but I couldn't help but feel that they weren't significant enough to justify being a separate buy -- I wish systems like the cards had been in the base game, while the expansion had focused on just giving us more of what was already present (especially more Explorers, as I enjoyed their variety and personalities).
But yeah, after owning, playing, and getting used to the game for awhile, I've gotten over most of my issues with it and am having fun. Like you said, treating it more like a board game is definitely a good way to play it.