I too am trying to get my head around IssueM. I'm finding it quite restrictive and there is little in the way of documentation to help those who want to customise the code. The shortcodes are limited and it doesn't look too easy to style them.

I'd like to make my own templates but there is no useful documentation on taxonomy. I can't work out if this is done on purpose or if they simply don't have time to put anything useful together. The videos, although a good idea, only cover the basics.

I keep giving up, moving to other options, coming back to it, giving it another go, and then leaving it again. I'll continue to explore other options as I battle through this but I'm guessing I'm going to end up looking elsewhere.