I read your whole document and I'm really damn impressed.
I've probably read a dozen different space-combat rule-sets and written almost as many of my own attempting to capture different themes (or getting distracted by sudden inspiration for a different core combat/movement/ship design mechanic). Yours is one of the simplest, mechanically, I've seen, yet I can see it capturing the feel of just about every system you have example ships for.
The power-based ships allows a ton of flexibility (reminds me of making monsters in 4e DnD). It did make me wonder if you created some ship-creation guidelines that you used to create (and ensure balance of) the ships or did you start by creating some examples and then figure you'd tweak them later?
One the Anal-Retentive, balance-obsessed problems I have with my own systems is needing concrete rules for ship creation before I make any ships (usually resulting in me spending so much time balance-testing every little ship system and re-writing chunks of rules that I never get any ships built to playtest and burn out or jump to the next project - but that's a different story). If you can just make ships and not worry about it, I envy you.
That said, will there be some form of "point value" or the like on each ship? Just looking at, say, the Star Destroyer and the Borg Cube, both Huge ships, I can't see the Star Destroyer having much of a chance against the Borg (though maybe I'm underestimating the damage output of all those TIE Fighters). I don't know if such a comparison is valid, but it's the sort of stuff I obsess (and burn out) over.
The system also has the (potentially huge) advantage of being "d20 compatible, so anyone using a modern/scifi d20 game could jump right in. I wouldn't imagine it would take a tremendous amount of work to create or house-rule some hero-skill-to-ship-effectiveness rules, to let the heroes personal abilities to influence the battle.
There were a few minor points technical issues and/or questions I had:
Fire arcs and hexes always kinda confounds me when testing systems. I tend to lean towards making the side arcs "double width" because I like the image of massive capital ships broadsiding and that's one way of mechanically supporting the feasibility of that.
How big a grid is this designed to be played on? You said "four times the size we used", but roughly what are the dimensions in hexes?
In looking at the explosion size of the larger ships, you'd need a considerably sized grid just to avoid being in the explosion of one of those, much less the (likely rare) situation of a couple of them going off in the same round. Unless you have a relatively massive battlemap in mind, a reduction in the explosion size (or effect) might be in order.
The potential speeds of smaller ships after a couple rounds of accelleration point to a fairly sizable map as well, and potentially a considerable amount of time spent moving each little ship its 10-20(-30?) hexes, figuring out when it can turn, etc. Sounds like it wasn't an issue in your playtest, so maybe I'm over-analyzing.
If you're going for pure cinematics and playability, I'd say set speeds are the way to go, maybe with an "Advanced Rules" section on the back for slighty more realistic movement. I've found in a Sky Full of Ships campaign I ran with my buddies over the internet, sometimes the semi-realistic movement detracted from the game more than it added...
Shields - It mentions in the initial definition of shields that they must be lowered for certain things, then lists two things in the "for example" area. It would be good to have a definitive list of "shield-negating" actions or to specify cleary in powers that shields cannot be activated in the same turn as a power.
What happens when a ship is captured?
I'm assuming the hero rules aren't entirely fleshed out yet since it's still in "beta."
The Star Destroyer has "AC" listed for its specifically-targetable areas. I really like the Star Destroyer's "footprint". Having it actually take up all those squares must make the scale differences dramatic and cool. Also, the color-coded specifically-targetable systems it neat. I started to tinker with a system that had no hitpoint/hull/structure points and instead had an array of external equipment (turrets, shield generators, armor plates, engines, missile systems, etc) that had to be blown through before you could target "internal systems" and have a chance of blowing the ship up. It ended up being far too complicated though(see attached image of a blank ship-sheet to get an idea of the complexity...)
Tractor Beam rules?
It would be useful to put a ship's boarding/marine effectiveness next to any "power" that allows a ship to board another. For example, the various Star Trek transporters. What does "capacity 6" mean rule-wise?
The Viper's "turbo" ability seems like it would be a pain-in-the-butt to keep track of when you have a couple dozen of those things flying around, even if they are in squadron. It instantly made me think of the last 4e game I ran where some Leaders cast a buff that affected a handful of minions - keeping track of which ones were buffed and which ones weren't was a pain and the "turbo" power requires, essentially, 3 tokens per Viper. What happens if you have a squadron of Vipers and each has used different number of turbo "charges"? I think could be worth allowing without any restrictions - it does take the Viper's
only action point to do it...
Didn't most of the Federation Class ships have rear torpedo launchers too?
Unless "cloak" will be defined somewhere, the Shadow Battlecrab's cloak technically allows it to be attacked while cloaked yet it can't fire back. The Klingon Bird of Prey was much more concise on this issue. Also, it's Absorbing Skin says it absorbs "energy weapons". It might be useful to add keywords or the like to powers to help adjucate powers like this.
The White Star's Interceptors - Is that 11 or more on the missiles roll or on a separate roll you make for the interceptors?
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That's it for technical things, hope you don't mind the long (and potentially nitpicky) post. This is all constructive criticism - I really think you have the foundations of a killer system here. I'm looking forward to seeing where it goes.
I envy your in that you have (presumably willing) playtesters! I used up all my "playtest tickets" with my gaming group and so I end up running solo-simulations with myself to test my games. My friends love RPGs, but none of them revels in playing (and even less playtesting my homebrew) space-combat games the way I do. Maybe I can get them to try out yours though since it's "semi-official" - IE, not made by me.
Nothing like a good playtest with some buddies to find the fun!
Keep up the good work!