I have both --- they're both great knives and perform beautifully as practical cutters.
It's really going to boil down to size and purpose. The Manix is pretty big and heavy. That doesn't bother me, but you just have to consider it carefully. Basically, IMO, when you carry a Manix, you've got to devote a pocket to it.
The Manix is the stronger knife, by a bit, but the Paramilitary is probably overbuilt for most EDC tasks.
You mention the size of the Para handle. The handle to blade ratio really turns some people off. But believe me, it's designed that way for a reason. I think it's a spillover effect of Spyderco's "little big knife" design approach. What you have is a handle that gives you full control and leverage on a modestly-sized blade. So, it's capable of heavy cutting, but also able to do very fine work that would not be as easy with a longer blade.
For me, thye compression lock is easy to use and provides a strong, reliable lockup. Some people incorrectly think of it as an upside down liner lock. It's much more reliable than that because that lock bar is not going to shift because it is being compressed. However, I think that the compression lock has a learning curve -- you may find it awkward the first time you try it, but after 10 minutes it becomes easy.
After saying all of those nice things about the Para, I've got to admit as fine a knife as the Para is, my overall preference is the Manix. Part of it is that I really like a knife that's way overbuilt. Also, although the Para's ergonomics are very good, the ergos of the Manix are outstanding -- the best of any folder I own. Another plus for the Manix is that the handle is drilled for tip-up/tip-down/left/right carry. The Para is strictly tip-down and right-hand carry.
So you've got a tough choice, but you can't go wrong with either. IMO, the Manix wins by a nose.