XC-305 was actually phasimg out in the end of project Babylon to XC-701B.
XF-100, the small one was also one of my favorites, pretty capable craft, it only lacked wast amounts of Dv, I remember that XC-305 had around 10.000m/s2? Which seems ridiculous :-D
Well, my vision of battle ship/mother ship of future is "versatility and modularity". All these crafts as great as they were/are had mostly just small docking ports to accomodate various missiles and torpedoes (but once I carried 2 small Sparrow shuttles form Zombiphylax docked to side ports of xc-305 or 701B). One great contruction point of xc series and its descendants was that the spine of the ship was made from girders strutted together, which made it quite stiff. I imageine future ultimate battleship/mothership as sort skeleton at its basic form. Just engines in the back, fuel going forward around spine made of girders, power generation (RTGs are too expensive in career mode, solar panels inefective in far way systems, so propably 1 rtg as backup, some 2 large panels and large power cell), massive torque (to compensate for carrying assymetric cargo loads), radiators. Keep it simple, keep it tidy, keeping parts count down, making it easy to refil fuel tanks - yeah finding and clicking fuel tanks under armor was always annoying with some ships.
So basicaly you would have this bare skeleton of a ship which would be quite light and easy to get into orbit and then modules to set it for particular mission profiles... Refinery module and mining lander, missile pods, science lab module, proprieatary SSTOs shuttles, dropship landers, hab modules for surface... I quite like Zekes "base in box". Some features are quite close to philosphy i would like to incorporate.
Armor, althou it looks auite impressive and quite nice, it has rarely any practical use so I just wouldn't put it there. Radical? Maybe...
So what you guys say about my vision? :-)