If I count correctly, there were 11 heroes in the base set. Looks like a grand total of 39 monsters, village cards, and heroes. I don't know how many were in Kongregate. Obviously, the more sets you have, the more variety you have, but because you always pick 4 heroes, 8 village cards, and 3 monster types, you don't have the same explosive variety that you get with Dominion.
I played a demo of Thunderstone Advance, and it was a pleasant experience. The storyline advances, and there are some new things. The Militia cards are replaced with Regulars, which are stronger and have a special ability with polearms, so they're not as useless. Advance also introduced something to the go-to-village, go-to-dungeon, or rest options. You can prepare, where you put any number of cards from your hand on top of your deck and discard the rest. It's like a perpetual Walled Village/Scheme for those hands where you draw dead. I'm considering getting Advance, especially since it apparently can be played with the original set, though the card layouts have changed.
Also, Advance now has rules where you diversify your village some more. You haven't more than X weapons or spells or mercenaries. This further reduces the variety, but unlike Dominion, it's possible in Thunderstone to get a combination of cards that are utterly useless and REALLY drags the game out. At least Dominion can always fall back on Big Money. There is not such thing in Thunderstone.