The news doesn't surprise me, though I do wonder why they made this decision before waiting for the December ratings. At least the show got one more season than
Firefly, and at least they get to give it a real ending.
You weren't missing much. Dollhouse certainly wasn't Whedon's best work.
Whereas I think it's his finest, most mature work ever. And I don't mean "mature" in the sense of adult-only or non-sophomoric, but in the sense that it's more developed creatively, conceptually, and thematically than its predecessors in Whedon's body of work.
For one thing, the exploration of morality in Whedon's work has been getting progressively more ambiguous and immersed in gray areas. More and more, his stories have been becoming less about good guys and bad guys and more about people making morally ambiguous choices for complex reasons, and
Dollhouse is the fullest, richest, most challenging development of that theme to date in Whedon's work.
For another thing, it's the most genuinely science-fictional series Whedon has ever done. Science fiction in the truest sense is fiction that postulates a scientific, technological, or sociological advancement and examines its consequences to human nature, society, ethics, morality, identity, and so forth. And
Dollhouse does that in spades. Once it got past its early "mission of the week" phase, it became a fascinating examination of the social, psychological, and philosophical consequences of the technology to overwrite or modify minds. With this series, Whedon has truly matured from using genre concepts as trappings or allegories for personal stories to actually engaging in fully developed science-fictional worldbuilding. And that's something few producers of genre television or film ever actually achieve.
However, those factors also mean that it's a difficult show for commercial television, maybe a bit too niche to succeed. I don't think it would be fair to blame FOX for this. If anything, FOX gave it more of a chance than it would probably have gotten on any other network, and I think they deserve credit for trusting in this challenging and unconventional show enough to give it two full (if short) seasons.
And it's not like the show's potential went unfulfilled. Heck, this show was doing the kind of big stuff in episode 6 that most shows wait until episode 13 to unleash. It had a bit of a slow start, but it packed a lot into its first season and it's packing even more into the second.