Maybe make hull sizes only mount weapons and defenses in an equivalent "tier" - tinies mount only the basic beams, smalls can mount up to lasers, etc (same for other weapons and defenses). This probably would need the techtree to be slightly restructured though.
Ok, as someone who generally likes things to make sense, be realistic, and follow a certain logic of "tidiness" (sp?), here's my take on how the Space Militarization branch of the techtree could have been made. It's not a suggestion, it's just an exercise, based on the premise that each weapon/defense type could/should be tied to a specific hull size - think of it as larger weapons not being able to fit in smaller hulls' hardpoints.
First, all civs should start the game with some basic techs, since they have been in space for some time now. Some have even warred among themselves, so it's rather strange that they have to research even the most basic of space weapons and defenses.
Those basic techs ("level 0") would have an attack or defense value of 1 respectively, and they'd be one-step-only items:
Particle Beam / Screen ; Space Cannon / Armor Plating ; Rockets / Chaff
Took some liberties here, namely creating Screens (basic shields), and Rockets (basic missiles). I dumped Sparrows, Stingers and Harpoons (and shifted the next techs to take their places), because this is not humans vs humans after all (even though some of the tech descriptions still assume the player is playing the humans...).
As for the techtree itself, it'd only need some reorganization to reflect the change with the basic techs. Some stats could have to be changed (including # of "steps" and/or RPs needed in each tech) to compensate for the reorganization. The connection between weapon/defense type and hull size would have to be introduced though.
So on tiny hulls you could only mount the basic techs plus the following "level 1" weapons/defenses:
Laser / Deflector ; Railgun / Titanium Armor ; Torpedo / ECM
On small hulls, same as tiny hulls plus "level 2" weapons/defenses:
Plasma / Shield ; Singularity Driver / Duranthium Armor ; Photon Torpedo / Point Defense
On medium hulls, same as small hulls plus "level 3" weapons/defenses:
Phasor / Barrier ; Graviton Driver / Tri-Strontium Armor ; Anti-Matter Torpedo / PD Combo
On large hulls, same as medium hulls plus "level 4" weapons/defenses:
Disruptor / Force Field ; Quantum Driver / Kanvium Armor ; Quantum Torpedo / Droid Sentries
On huge hulls you could mount any weapon/defense.
Again some liberties. For the sake of going with the rest I changed Kanvium to Kanvium Armor and Photonic Torpedo to simply Torpedo (also to avoid confusion with the Photon Torpedo).