Many of the issues mentioned in the OP are mostly due to the stage of the alpha build. While it isn't wrong and nor is it unnecessary to point out balance issues and ways that make it easy to acquire ships, it should be noted and reminded that this is campaign is literally in place so we could at least play the campaign. The final version will obviously be radically different, which will change the balance issues, the mercenary issues, the 78 ships (exactly how many FP over the limit are you with that, mineplanet?) in a single fleet, etc.
As for point three, I'm not exactly sure what the OP is asking... taking direct command of fighters I assume? If that's what was meant, then the answer so far as been a no on that ability.
Point four, it's hard to know exactly what the issue is without knowing all the circumstances like what other orders have been issued, what ships you have, what the enemy has, etc. So many variables to take into account before saying that a ship just completely ignored your orders, since some orders actually give/allow ships to have some flexibility to defend a point, because they'll engage at some distance from the point in order to defend it, rather than staying virtually on top of the point and unable to actually move because that would limit a ship's capabilities. On another note, when ship officers get put into play with personalities, you might actually see ships REALLY ignore orders. It's debatable on how officers will work exactly, but it's something to take into consideration... that being you may not get 100% control of your fleet at all times.
Point five, I don't see why people are trying to get 'extra' OP for having unused weapon slots. In a way you are already getting OP by not using that hardpoint or turret because a weapon is not taking up the OP space. Why would you get extra OP for not spending OP? It makes no sense to me. If you choose not to use something, then you benefit from the unallocated OP. No reason to get rewarded twice. Having ship designs be a little more flexible in terms of having designs where you don't utilize every possible turret/hardpoint allows customization for playstyles or whatever role a fleet that particular ship needs to fill.