Ben, first, let's make sure we're using the word 'template' in the same way. Each Resource has only one template, which is stored in the DB in the Resource's 'template' field. So, the only things in MODX that you call templates are in the Template section of the Elements tree in the Manager and only one template will be involved in the display of your page -- the template of that page (not the templates of the posts you're aggregating)..
It sounds like you're talking about Tpl chunks, or something similar, if every resource rendered by, say, getResources might have a different format.
I think I understand what you want for output, but how are the Tpl preferences for each resource set? Can different users have different formats for the same resource?
Using getResources might be possible, but how will you know the Tpl chunk to use for each resource *before* getResources retrieves them?
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PLEASE, PLEASE specify the version of MODX you are using.
MODX info for everyone:
http://bobsguides.com/modx.html