I think you guys make one fatal mistake: you don't consider teamwork. Situations like "lone-mentu-attacked-by-Rakshasa-and-blown-to-bits" can't happen. Let's consider situation with one GTVA fighter wing+Mentu vs one Shivan fighter wing+Rakshasa. GTVA will win. Why? Because Rakshasa's beams won't do anything to Mentu, the most heavily armored GTVA cruiser. Mentu will eliminate Shivan fighters with GTVA wing's help, then fighters will disarm Rakshasa and slowly put it down. As c914 said "capships for everything are for nothing". 3km universal superdestroyer *will* loose against team of smaller specialised warships. So putting SVas to Aten/Mentu or 100-fighter hangar to Orion MKII (anyway next Orion is VERY hypothetical as technologies will be probably completely merged and next-generation GTVA fleet will be common for both Terrans and Vasudans) isn't good idea. If you don't believe me, we can do little wargames on ICQ/MSN/IRC.
BTW little digression about current non-beam and non-prototype weaponry that could be given to capships:
- Subach/Mekhu - better than standard capship turrets but MS would be much better
- Morning Star - one of the most powerful AF weapons, low energy usage (comparing to flaks or AAAs, however also two times larger usage than Prom S and 18 times more than standard turret but considering old age of standard turrets and incompatibility with modern systems changes things for better) gives it possibility for wide use on all capships, is quite good against shields, has got large range (2000) and, the most important, it deals serious kinetic push, I think almost all GTVA capships should be armed with it (mostly AC and Carrier-oriented) as it's very good in fending off fighters and shooting down bombs
- Akheton SDG - could be good in AC self-defence, but has got large energy usage and much shorter range than Maxim (750)
- Prometheus S - good weapon, 1500m range and less energy usage than Morning Star but becomes obsolete as MS+Maxim duo can do the job better
- Maxim - another very good weapon, VERY long range and large hull damage, altough energy usage even bigger than MS (three times as much as Prom S) note about modern systems applies to it too, weak against shields but MS can do this job, also can be used as AC self-defence
- Kayser - I think it's even worse for capships than Prom S, energy usage as large as MS and shorter range (1500)
- Circe - unnecessary crap with not-so-great shield damage and short range
- Lamprey - as above, could be good for fighter suppression if it had larger range, less energy consumption and EMP effect on impact
- Terran Turret - C.R.A.P, can't do anything to fighters, better against bombs, but it's very old and becomes incompatible with modern systems
- Terran Huge Turret - C.R.A.P, more damage but even less velocity than standard turret making it even more useless against fighters
- Terran Turret Weak - C.R.A.P, nothing different than standard except very few shield damage = even more useless against fighters
- AAA - very large energy usage limiting it to capships only and IMHO should be used only on AF/universal capships, anyway it's powerful due to shield penetrate abilities, overloaded version with 4000m range, rapid fire and damage enough to blow up Seraphim in two shots is the best AF weapon
- Standard Flak - quite powerful weapon, altough without ability of shield penetration and takes more place, it deals more overall damage per second and is better in fighter suppression, also good for AF/universal capships
- Heavy Flak - weaker counterpart of Standard Flak, can be used when Standard flak would take too much place (like in Aeolus with two UltraAAAs)
- Long Range Flak - basically LR version of Heavy Flak, IMHO useless, Maxim has got bigger range
- Rockeye - this could be powerful weapon for capships, rapid fire, long range and seeking ability would make it good weapon for both fighter killing and suppression, in theory it could "spam" and force enemy to either turn back and launch countermeasures or face with lots, lots of rockets
- Tempest - short range = unnecessary crap
- Hornet - like Rockeye good for "spamming", but shorter range and less maneuverability makes it less useful, it's also older and less compatible with modern systems
- Harpoon - like above, only with better maneuverability and better compatibility
- TAG X - gives better accuracy, but it'd be much better to give it to fighters rather than waste space on capship
- Stiletto II - pure AC self-defence, with rapid fire and 5500 range (1500 more than typical beams) it can disarm enemy capship and is more place&energy-efficient than Slash beams leaving more place&energy for other weapons, good for specialised capships (AF cruisers or carriers for example)
- Infyrno - AF weapon with the biggest damage, takes lots of place limiting it to large capships and has short range, however no fighter or bomber can survive when hit by it, also good for disarming capships that will get too close
- Cyclops - C.R.A.P, less range, damage and fire rate than beams, not to mention it can be taken down
- EMP Adv. - short range, but great for anti-bomber defence, good fighter supression weapon.
