Yeah, hierarchical tree-views suck. In the nightly builds (soon to be betas for v3) tags can define a hierarchy by including slashes in their names. They're also browsable in the toolbelt, which is just like 0.10's side-window. It's mighty close to what you were used to.
I see the Toolbelt - I'll try it out and see if it gives me similar functionality. iTerm 1 has a ton of bugs that bother me so upgrading would be nice.