Both are excelent knives, you'll probably end up owning both if you're into Spydies. It's just a matter of which one to get first.
What I love about the Military is that you get a lot of blade and a well thought out G-10 handle in a very light weight package. Flatground Spydercos are my favourite users, my Military has been with me for quite some time and has worked very hard for me (it was one of the first modern folders I bought). It's beat up, I had to reground the tip, but the lock-up is as solid as ever. If you like longish blades on folders and have big hands, you'll love the Military. Nowadays, my regular Military is half retired and I carry the Ti version more often, just because it's prettier. If I had to criticize something, it'd be that the clip has a single position and it doesn't carry very deep.
The Paramilitary 2 is probably one of the best design revisions by Spyderco. I've got the Para 1 and love it, it was my only knife for months while working at archaeological digs abroad. It had some things I wasn't crazy about, and they were all addressed in the excellent Para 2. The compression lock is arguably better than a liner lock, but I'm not an expert on that and use a lot of different locks without problems (except for a couple of Buck liner locks years ago). Mine had the tiniest hint of side to side play, but it went away after tightening the pivot (somebody less obsessive than me would probably not have noticed it).
In use, a Para 2 and a Military will perform just about the same. I mean, both have similar flat ground S30V blades. The Military has a slight advantage (for my large paws) when wearing gloves since it has a longer handle and the lock is easier to disengage. They also feel about the same in my pocket, when closed their width and thickness is almost identical, the only difference being the Military's longer handle (the difference in handle lengths is much more noticeable than that in blade lengths). Also, my Militaries are smoother than my Paras, my Superhawk is the only buttery smooth compression lock Spyderco I've got.
It's a difficult choice because there's really no wrong answer.