1) Do you think the amount of influence the player has individually over the battle is in a good place this patch?
Are you asking if the player ship has enough influence, or if the player does? If it's the latter, there's a lot of variables here, too, from ship loadout to officer choice to orders given, so it's a bit vague. I don't think you mean pre-combat decisions, but aside from that, I'm not actually sure about the scope of your question.
Although, regardless of the answer: I think it's in a pretty good place right now
The player ship makes a good impact even w/o any skills, so anything it gains from said skills is a bonus in that department. It doesn't always have to be direct damage, but also creating openings for other ships.
And the orders - especially eliminate - allow for some decisive control, which was not an option before.
2) Do you think the player should have more control over friendly AI to make strategic decisions (i.e. flank this ship, engage this ship) or should the players role be primarily to fly their own ship and let the AI do its thing?
My feeling is that the player should give a few orders now and again but should mostly focus on piloting. There's some room on both sides here - a few more orders and more time spent in the combat map, or just giving orders once at the start and not worrying about it from that point on - but ultimately the game shouldn't make you want to check the map all the time. Not "never", but not to the degree where you're giving tactical orders and need to check on their execution a few seconds later.
As you say, the number of command points available and the rate at which they regenerate - and the means to influence it - are indicative of the design intent.