pathauto + hierachical catogry + single level

Not currently possible due to pathauto limitations (or more specifically the token module I think).

As far as I know (things may have changed recently) pathauto can't create aliases for taxonomy combo urls - eg: /taxonomy/term/x,y,z or /taxonomy/term/x+y+z etc. You could always create your own module to generate the urls though (or create them yourself manually if there is only a small number).

I think Taxonomy Filter might work for you if you can create all the aliases though (bearing in mind that each taxonomy listing might need multiple aliases to account for differences in term id order).

Taxonomy Filter looks at the underlying URL for its parameters rather than the aliased url, and it looks for aliases for all the urls it outputs in its block. That makes me think that as long as your could create all the aliases correctly, it should work.

You could always test it with a few manually created aliases to see whether a) Taxonomy Filter parses the url properly and shows the correct tag cloud, and b) whether all the links in the cloud use the correct alias.

Another point: Is a tag cloud the best representation for a hierarchical vocabulary?

Thanks Styro, to answer your very last question the tag cloud would be used only for the single level vocab, which has 5-6 terms only, hence the tag cloud would be ideal for it on the hiearchical vocab pages. The hierarchical vocab will be used with taxonomy breadcrumb and taxonomy context in addition which seem to me an ideal and highly customizable way so far for browsing a hierarchical taxonomy :)

I will have to reread your post a couple of times until it seeps in :)