Appreciate your feedback!
Fighters
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Fighters seem to lack a hard, asymetric counter. The best way to counter a force which relies on fighters is to have enough carriers with intercepters in your own fleet. Not something you can refit easily! I tried creating a pure anti-fighter destroyer and cruiser, but they were barely able to hold their ground, even with lots of double flak cannons.
It's hard to say without knowing what you're looking at - is it a 1-1 type situation, or a fleet situation? Fleets in general can counter fighters, but it takes giving good anti-fighter capability to a bunch of ships.
Flak actually isn't very good vs most fighters; PD in general is good for anti-missile, but anti-fighter is a different beast. In particular, PD that does kinetic or frag damage is really hampered even by fighter-level armor. Stuff like Phase Lances, Tactical lasers, or even Light Assault Guns is likely going to be more effective. Locusts are great, too. And the Doom - while unique in that - is about as close to a hard counter as it gets.
Big Battles
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Whenever I got to the deployment point limit, I felt screwed over.
When I defended my station, I was able to add maybe 30 points to the station, but when I attacked a Luddic Church base, they were fielding an entire army in addition to their station.
Not to mention that in such large battles with station, my FPS drops and it feels like a lot of inputs get dropped as well. Makes for a very frustrating experience when you can't tell why your ship won't move backwards - unless you switch on the AI and let it handle your flagship.
So there should be a way to control the deployment point limit, a preview of what you're getting into, and a chance to back out.
(Right, there's battle size in settings, as someone mentioned. Basically, the bigger side gets the bigger chunk of it to deploy stuff.)
I don't think it's possible for inputs to get dropped - well, I guess anything is possible, but it's definitely coded in a way that should avoid that, and I haven't seen it myself in low-FPS situations.
Is it possible you're holding down too many keys at once? For example, if you're holding A, S, and ... let's say X, or another nearby key, chances are your keyboard is only going to be capable of registering at most two of those presses. That's just a physical wiring limitation on most keyboards. If anyone else is seeing input be dropped, I'd be interested in hearing about it.
This probably isn't 0.9 feedback, since before I never ran such large fleets, but not being able to back out because my fleet is too large was quiet the shock. In a game that's supposed to be played on Iron Man, I hope the fleeing mechanics get a full overhaul.
I've got a TODO item to look at it! In the meantime, you could deploy some stuff, lose it, and then retreat - not a particularly elegant workaround, but it's there.
Best addition ever, but on the other hand, having to defend them is a big pain. Being able to bribe them off is a good idea, but not always an option. And having to sit around your colony for 30 days and hold shift is very boring.
Having the option to leave part of your fleet to defend your orbital station would be good, as would the option to limit outside trading with other stations so this problem doesn't arise in the first place.
Other factions should have to wait until you establish Commerce to trade with a planet.
Often, I don't want a whole colony, just a hidey hole to store all the gear I have amassed without paying the 1% monthly fee.
Tweaking/tweaked a number of things here. For the time being, though - if you don't build up a colony beyond a spaceport, I think you should be able to have a hidey-hole that doesn't get harassed - it might not even have positive population growth, but even if it gained a couple of size points, I'm not sure it'd get to the point of being noticed.
WHERE IS 0.9.1 OTL
As I mentioned a bit back, I got sidetracked by some hardware issues, plus there's just a lot to do for .1, but: back up and running, and making progress

Maybe I should post up some in-dev patch notes... hmm.
(OTL?)
And I found that most of intel things are hard coded, do they mean reports.csv is totally useless now?
And that's a disaster for translation, whether vanilla or mod...
Yeah, reports.csv is no longer used. It's just really awkward to put together dynamic text while pulling strings from there, so it's all in code. I thought the translation effort had some automated way of pulling strings from class files, though?