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After playing enough, I do prefer dominion to this game. It was a good attempt, and the theme is great, which is why it still sees some action here. My main complaint is that the game goes on for far too long after your engine is working. Dominion ends at the right time.
The game has a much stronger theme and a more interesting scoring method than its predecessor. Because you have to choose between preparing for battle or actually battling on every turn, you must balance your deck between being strong at deckbuilding and being strong at scoring points. The abilities of the cards are probably about as varied as the core Dominion's mix of cards, but knowing how much preparation you need before going into battle is thematically fun and strategically interesting. Now for the part of the comment where I whine. Parts of the game seem unpolished. Several times during our inaugural Thunderstone session, my fellow players and I just asked each other "Why is this card worded like this?" or "How is that supposed to be a balanced card?" (though we haven't played much, so this one is just a n00b's opinion). Unless my group just evaluates cards and wording differently from most people, these seem like avoidable problems. The other problem I have with Thunderstone is the cards themselves. First, why XP cards? They don't add anything, and I would rather just have cardboard chips. Second, although the art is pretty good, the cards themselves are rather poor quality (many stacks were starting to warp as soon as we took the plastic off!). If you're going to sell a card game as a big-box game with a big-box price, I'd appreciate it if you at least made sure the cards were high-quality. I love the theme, I love the dungeon/village division, and judging on core mechanics, I'd call this game Dominion's equal. With some higher production values and some minor tweaks for balance and wording, I would probably rate this game a 9.
The game is not actively bad. But (to bring comparisons to Dominion), this game was not properly developed. Design = great. Development = the crapper. This could have been as good as Dominion, or even better, and the game gone through proper development time. As it is, clumsy AEG rules, and unclear definitions make this less fun for me.