Actually you can have any number of different layouts for subcategories, you just need to build the templates. I have different templates for my About, Archives Index, and Photos pages. You simply make a copy of index.php for each, rename it to say archives.php for your Archives Index, customize, and then modify the category
mod_rewrite rule so that archive directories use say archives.php instead of index.php.
Not trying to single you out, but I think a lot of users coming from MT have difficulty picking up the WP architecture and the
mod_rewrite rules. These rules essentially serve the dual purpose of specifying the directory structure of your archives and which template to use. If you peek in the .htaccess you'll see that every archive rule makes use of index.php. Once you change that to another file, you've begun using a new template.