I love Investigations. Don't get me wrong, it's clearly a load of stinkin' pap with numerous holes in it but I enjoyed the whole Seska spy arc and the attempt at serialised storytelling. Maybe I'm blinded by my fondness for the thing.
It is of course ludicrous that Janeway allows Tuvok to entirely undermine Chakotay by keeping him out of the loop. Aside from highlighting her lack of trust in him (in general or just his acting ability) it also demonstrates that Tuvok is actually Janeway's true second in command. Chakotay must have felt like a complete lemon.
In the end, it turns out to be an utterly pointless plan anyway since Neelix was on the cusp of finding out that Jonas is the spy with significantly less effort. Tuvok's plan is moronic, convoluted and entirely dumb. Instead of an enormously complex performance that requires Paris to play malcontent for months and Chakotay to be treated like an idiot, why not just have a much better security officer with a much better plan? It was completely ridiculous. Neither Tuvok nor Janeway come out of this with much credibility.
I agree that the motivations of Jonas are bewildering. What does he get out of this? Assuming Seska succeeds, his best outcome is a place at the grown-ups table in the Seska dictatorship.
Entertaining stuff if entirely silly. More Seska would have been nice.