I like WIndom a lot, and the disturbing atmosphere of his cabin (idyllic? psychopatic?).
The reason why some people don't like him seems obvious - too big the expectations (the exposition of the character at the end of Ep.21 is fantastic and lives up to any expectations raised by Cooper's praising his genius).
Windom really seemed kind of "unserious" when he moved on to tame Leo in those filthy pyjamas of his... hmm.
The biggest problem though was best noticed by Crabalocker:
I think his character suffered for having to 'carry' the later half of series 2 once it had lost it's sense of direction.
yeah... it would make a great subplot but it couldn't have made a good enough follow-up for the who-killed-Laura mystery...
However, the Windom character played a very important role in the development of Cooper's character. 12rainbow noticed it very well:
But Windom is there to show us that Cooper is not, as Hawk says, "fearless in this world,"
Exactly so.
Note that at the beginning (esp. Season 1), Cooper himself seems to be some superhero and his mind clear as a diamond. The more he sinks into the everyday life of Twin Peaks, the more humane he seems - yet, he still remains a man of superb intelect and great strength who knows exactly what he wants and how to get it.
And then - he becomes weaker. Vulnerable. And that is very closely connected with Window and their common history.
The confrontation of Window against Cooper makes Coop look like some young boy playing in the yard. Like he says himself, if Windom wanted to kill him, he'd already be dead. He realizes it and can do nothing about it at all....
Bobi 1 Kenobi
B. Beware
O. Of
B. BOB