Thanks for the feedback, there was an omission with the Stun Rod indeed, it used to work (shoddily) in October 2014 but no longer does. Fixed and will be updated in the next version.
Sadly, wielding an off-hand weapon only influences the accuracy of 2-h ranged weapons, not melee weapons. I could make a feature request for that (as it seems logical), but... the Devs are very busy right now and I don't want to pester them with such a minor detail.
As for missions - this and much more will be possible once the TFTD mission support will be added (which is soon), we'll see what we can do then. Nowadays we're stuck with what we have - I plan to add more easy-plunder missions, but it's all up to the Gods of Random. It's impossible to tweak mission chances on montly basis, so you're as likely to get a Mercenary Assignment on January, as you are 2 years later - sam goes for the Passengers Freight. And the first enemy mission in the game is *always* an Academy Daily Operation in the proximity of your base, due to hardcode (I actually like it, it teaches the player a lot)... but I agree that the difficulty could go lower after that... at least if you pick your targets smartly.
I'm planning to at least postpone the widespread appearance of stronger races (CoS, Mercs, Star Gods) till much later in the game (but you will be always able to encounter them in a race-specific mission or a knee-jerk Retal, even in January, if the Gods of Random really hate you).
Oh yeah, and the difficulty is intentional
I don't want to ramp it up to a level where it takes away any fun... but just a notch lower would be ideal.