I would like to document this. This extra text could probably be displayed underneath the current name of the theme (to be honest, I try to put the context in there now, which his not pretty and most of the time the text is topped off)

Reference material: this is a second thing that I miss. I would like to put a link to where all the reference material for this theme is put. (e.g. wireframes, wiki, whatever)

Just one link.

This could be part of the theme description, so then no other extra field would be necessary.

So instead of the name field for the theme, make it two fields: a name field and a description field. They are just put under each other. Most of the time there is plenty of text space there. And you could always consider a '-' one can click on to hide most of the description text.

I really love the minimalist approach, but I also want to be able to work with easybacklog as my command center. From where I have a total overview of what I find important to work on and from where I can easily reach all info I need.

But maybe I just misinterpreted the themes concept? 

Themes for me are big blocks, that help me discuss the features with the customer, help me brainstorm and put them in a big functional context.

But these themes-blocks are too big to put them one after another. That is just waterfall again.

I would like to be able to put a weight factor in front of each story. This could be a free integer field. Just let me fill in a number (I can choose big numbers to leave space for incoming stuff etc) and make it possible to sort on that level. This would result in a view with all stories ordered on prio level and with the theme field just as an info field. 

For the moment I too am coloring the user stories, but this really is not a practical way (+ I want really one clear order, not 20 items with prio 1)

Voila, hope this is a bit clear. Always ready to give some extra clarification of needed :-)