"In my 23 years, I have never ever seen anything like this. We saw it the other way in 2001. I mean, you have to ask yourself, 'How did the Mariners win 116 games that season with that roster, compared to this roster?' This is just as inexplicable the other way."
--Mariners president Chuck Armstrong

Chuck Armstrong doesn't see any relevant differences between the 2001 Mariners and the 2008 Mariners.

Without even looking them up, a few differences spring immediately to mind:

1) The 2001 team played far better defence than the 2008 team, both infield and outfield.

2) The 2001 team was a far more patient hitting team, drawing vastly more walks than the 2008 team.

3) The 2001 team hit for far more power than the 2008 team.

Are there any I missed?  I bet there are.  Statistical evidence for your points and mine would probably be ignored by Chuck, but feel free to post it anyway.