They haven't made many games but I'm a big fan of Acquire.
Tenchu was excellent and finally brought the stealth aspect to ninja games. Tenchu 2 was a disappointment but probably could have been great if more time was spent on it.
Way of the Samurai is one of the most innovative games of this era. It's very open-ended for a Japanese developed game and an awesome beat 'em up/adventure/RPG hybrid. It's not for everyone but I loved it.
The weird thing about their games is that people seem to love them or are completely indifferent to them. Magazine reviewers almost always give 7's to their games.
With the Tenchu series now under a different developer, it will be interesting to see what Acquire does next. What do you think of them and what kind of games would you like to see them make?
