Hey, and welcome to the forums!
Or, rather, welcome to posting on the forums.
It's good to see you here.
Josh has never quite seemed 100% sure on how research will work - he's moved between a few different ideas. The last idea he mentioned, though, is that there will be limits to all things, and researching one thing will degrade others. For instance:
Shields: 5
Engines: 7
Weapons: 3
The above could have its weapons improved to Weapons 5, but that would cause Shields and Engines to decrease to 4 and 6. Increasing weapons further, to our arbitrary value of 7, would pull shields and engines down to 3 and 5 respectively. You could keep going until you got to Weapons 13 (your solid pulse beam, essentially), but Shields and Engines would both be at 1.
That's the last I heard, anyway, He may have changed his mind in the past few years.