Okay, I rented (netflix) Smallville season 5 on HD DVD moved on to Season 6 Saturday. What happened to the special features?
they weren't much to begin with but at least Season 5 has PIP commentary and a visual break down of some special effects. Only some of the other shows in season 5 had commentary. Most importantly the Vampire Halloween show where they apologized for making it. As they should. ;)

Season 6 nodda, nothing so far. No PIP and no commentaries. The Green Arrow specials don't impress me all that much.
What happened between season 5 and season 6 HD DVD release? Why did Warner cut the special features?

My guess and forgive me if I'm out of line here but my thoughts were that they "dumbed down" the version so that it would be the same as the Blu-Ray version. There was never a season 5 released on Blu-Ray. But none the less they could have added more to it. I don't recall if it did have any commentary tracks on it, but an In-Program Experience like they did for season 5 could have been pretty cool.

I didn't know Blu missed out on season 5.

The DVDs don't have much in the way of special features, but normally they have at least 2 episodes with commentary. Season 6 is a departure. I don't know if the DVD version is any different.
Amazon list the DVD edition as having 6 disks, HD 5 and blu 4. I don't know if that is correct either, I could find out through netflix but I didn't want to screw things up by changing my preference.

I was looking forward to PIP for at least one episode in season 6.

For now I'm going to agree with the dumbed down for Blu theory. Maybe an insider know the whole story and will share it with us. (hint, hint) :D