Stefan, although it is true that you cannot have more than one project open in Analyzer at a time, you can run multiple instances of Analyzer at the same time, with each one having a different project open.
After you've got one instance of Analyzer open, start up another instance. In the second one, open the second project you want to examine. Then you can place the two Analyzer windows side-by-side to do your comparison.
BTW, running multiple instances like this is possible with any MadCap program. I often have two instances of Flare open at the same time, each with a different project loaded.
I don't know of a limit as to how many instances of Analyzer you run simultaneously, but I think the practical limitation will be determine by the amount of memory your computer has to load all those applications; at some point, it'll run out.