I agree that not having the Prefereces... command is bad, in that it's confusing.
Having said that, I understand why it's not there.
So, to please both camps, have the Preferences... menu item launch a help window/assistant that explains the preferences philosophy of TextMate, along with visuals on where to find them (the specific menus), and how the TextMate approach makes sense for what TextMate does.
That will eliminate the number one problem encountered by new users, and also get them quickly up to speed about TextMate's underlying philosophy.
"Show, don't tell."
Regards,
Eric Ocean