PRO-TIP for newbies:
The ignore button is your friend.
Caveat: If you get offered a proper tactical mission, you should accept it (assuming you have the troops). They don't last long (I think some disappear immediately) and you'll either get some penalty or miss a big reward if you ignore one.
Otherwise hit ignore. You really don't want to waste time travelling to every new resistance lead that turns out to be "scan for 7 days to get some alloys". That stuff can wait until you've finished your current scanning. In many/most cases they are not worth doing at all, ever.
These missions do not affect your reputation, they are just options for getting bonus stuff. The missions don't last forever, but there is no rush.
On a third campaign. Built Advanced Warfare Centre ASAP. Have had dozens of level ups since then, with zero bonus skills. I wouldn't even mind if I KNEW what the odds were per level up.
I think every soldier gets one skill, given at a random level.
I'm 90% sure it's retroactive too (so long as you aren't a Colonel yet), since levelling up my Cap./Maj. guys has a very high chance of giving a bonus skill, while Cpl/Sgt generally don't get anything.
My ranger just got the "kills refund the action point" sniper skill. I wonder what happens if I combine that with Run'n'gun and the "free sprint after a kill" skills.
I love how the balance in this game works by making everything 'overpowered'. Picking between the various 'overpowered' options is much more interesting than picking the boring "+10% to X" upgrades in most tactical/strategy games.