My first stab at the game (which I still haven't gotten to chapter 4 with yet, despite having put in well around 28 hours into it...) I tried focusing on beams and shields (or, "Shields and Zaps", as I labeled the save slot), thinking that might be a good idea.
To some extent, it was alright. But the game has been kinda pissy with me as far as blueprints are concerned. So I've generally been aimlessly wandering around the "lesser" systems trying to hunt out the technology that will let me even consider getting past the 60-level warp blockades, despite my ship being level 75. It took me until the start of chapter 3 before I could even get point defenses, and this is supposedly a high-availability gen.
I'm still hunting for that last piece of my holy grail, the fusion beam. Even with all my boosters and fixed turret upgrades and triple huge and all that jazz, overload emitters can only get you so far.
I suppose it was a mistake to not have invested heavily in launchers in order to give me some decent hull damage, but when the game started out I took "You should really only specialize in one or two areas" to the extreme, putting points exclusively into beams and shields. And now both of those are maxed out (for me, at level 8). And the few "Just a few points here" sidelines I had are now also either maxed out or very close to, including maxed hull and crew, high-level turrets and reactors, and a smattering of points each in armor, engines, and bombs (I *LOVE* bombs, and they've helped me win a few tricky battles, but I've learned since then that I just can't expect to specialize in them. Far too unwieldy and prone to friendly fire, destroying either my own ships or pissing off those of an ally I've spent ages getting good relations with).
Boarding is hysterically good fun and has been incredibly lucrative a few times, netting me double the black box info on some juicy ships, but the cost is (funnily enough) astronomical and cannot really be used as a standard in most battles (also, NEVER let the AI take control of your boarding ship, or expect to lose hundreds of goons to a pathetically meaningless death as they're catapulted straight into the enemy destroy-all-humans beam).
As it stands, I don't really have anything to take out the higher-level encounters. I can't annihilate the swarm of ships that gang up on us unless I can take them on mano-e-mano and have a lot of time to do it, and I have nothing to counter the masses of ion emitters (which I ALSO can't find the last blueprint for) that result in my ships having their super-duper-pooper-booster shields stripped away instantly and then held down under the barrage of fire until they just pop.
The way things are going, basically my only achievements have been unlocking every single tiny, small, medium and large ship design, and two of the huge buggers. Also, I've found out which ships make for good resource gatherers (hint: Hammerhead with lots of hull boosts can stock 1200+ rez, while sporting great maneuverability and two huge turrets for concentrated zap efforts at mining stations. They can also pack a couple decent-sized tractor beams).
And, as others have mentioned, the AI-controlled ships are piloted by rejects from the chimp space program. This means I can't rely on them to actually do any real FIGHTING, and instead kit them out to perform such noble and valiant roles as "decoy" and "critter-cleaner", or simply stop rebuilding them during a fight to save rez and goons. Otherwise, I just stack them to the rafters with shield boosters and then plug a single leech emitter onto them so they can at least slow down the tide of incoming death.
EDIT: Aaand I'm an accidental necromancer. Whoops.