The nice thing about Primeval is that the plots just aren't that complicated -- if someone seems fishy, they probably are. And on television, at least, I'm pretty sure that all public/private partnerships are bad and wrong.

I do want to know what Matt's story is, and how is it that he's been preparing for the ARC since it's only been around for 4-5 years.

I hadn't caught that; maybe there is a cool time-travel related explanation! Or perhaps you are looking for too much continuity in a show which is not exactly known for its coherence? I know that that's what I'm doing when I complain about the S1/2 reset being ignored...