You have a SIGNIFICANTLY higher chance of winning with auto-resolve if you take personal control and then kill the most dangerous ship(s) and then auto-resolve, at least from what I've noticed.
I don't know specifics, but each ship seems to have certain odds of winning, and if yours are higher (combined, including but not limited to: your level, what you've put into your character, your ship, guns) you win. Not the best way to describe it, but a good case in point: Take an Unsung, from Neutrino Corp (Mod). Use it at lvl 1, with crappy equipment (don't fill it up all the way with equips). You get rolled vs most fleets. Then, take it again at lvl 40, with good equipment, etc. You can roll fleets with auto resolve without a second thought. Just what I've noticed.
Edit: And to add to your statement about them getting away with second in command; yeah I've noticed that too. Also, I tend to auto resolve (esc > leave battle) before the battles end all the time when I manual control because even if things 'retreated' when you auto resolve after routing them (before it actually ends) you will end up having destroyed all of them and potentially have more boardables.