Congrats for uncovering King Abdullah! :-) He is a huge Star Trek fan (they're opening a ST theme park near Amman soon, I gather).
I have a higher opinion of Investigations than R. Star. I liked the idea of a macro-plot that develops over 4 or 5 episodes -- they don't happen very often on ST. I also thought it followed nicely on Threshold, and Tom's confession to Janeway that he needs to prove himself. I have this theory that she conceived the plan with Tuvok very shortly thereafter -- in a somewhat calculating way (as in, "he'll do anything ..."). The dynamic between Tom and Chakotay should have been explored better though -- ultimately it was Chakotay who was betrayed by Janeway, who didn't trust him enough to involve him, and the only one who ever really apologizes to him is Tom. (I did write a short story on the C/P dynamic early on in this sequence, called "Far From Home".)
I also liked the awkwardness of Tom's apology to Chakotay. Some people would say he was an ass about it, but frankly I think he just doesn't really know how to act as he's been put between the command team and really was in a difficult situation. He's also used to being a failure, so being lauded as a hero is great, but he's clearly not entirely believing it. So he turns it all into a grand joke -- as he tends to do with most things that matter to him -- and Robbie McNeill is a good enough actor that you can see in his face that it's not a comfortable one.
As for Jonas, he was a serious failure as a spy. In one of the previous episodes you see him communicate with Seska and the Kazon and he is just such a bumbling moron, a real amateur when he tries to impress these people. So I wasn't surprised when he totally overreacted with Neelix throughout the episode. Basically he's a little shit who's in way over his head.
Neelix? Yeah, irresponsible journalism 101. Right up there with Wikileaks for putting people in harm's way. I do, however, like the way he brushes off the Doctor and his ego as a running gag.