I'm confused - you said you write up a fully detailed analysis when you have 1 or 2 options (in your comment to John) but then you mention (in the question) that you compare the pros and cons of 3-4 alternatives. I'm guessing the pros/cons aren't fully analyzed?
Since you're combining your Requirements and Analysis in the same document, I'll assume that you've got the full use cases in the first section and then you address them in the Analysis section. I would leave those two sections as is and then add a third for "Other Candidate Designs" or something and then just list the reasons why you didn't choose it. This can be very brief and not require the UI design etc. However, if you've already done mockups and THEN realize it won't work, you could probably include them in the doc. A good goal would be to make sure that the focus of your doc is still on the design you're using, but include sections for those curious about the rejected designs.
As for having Structure and Consistency, we've been using the Rational Unified Process documents for Software Architecture (the SAD). Here's the first link to a template I could find: http://www.cs.toronto.edu/~wl/teach/407/2002/rup-sad.html
The idea is that you break down the system into different "views" and document them. This is heavier than your current document, but some of our clients require the extra documentation so we provide it in this format. Using the RUP SAD you could list your rejected designs in the Architectural Goals & Constraints section or in a special section at the end (which is what we usually do).