I'm not quite sure what you are asking. So please post back if you need more information, or if I'm heading off on the wrong track!

You know how to use
MTEntries category="A OR C" to show the entries you want?

Recent Entries (ie links to the last 5 entries in that category)for each category you could do like this:
CODE
<MTEntries category="A" lastn="5">
<a href="<MTEntryLink>"><MTEntryTitle></a><br />
</MTEntries>
- and the same thing for category C, changing the A to C, of course!
If you want to exclude specific categories from an Archive listing using MTArchiveList, I think you'll need the
Filter Categories Plug-In.
Unless anyone else has an idea, the other option would be, of course, to simply code in the actual links to your category archives...

Does that help?