I've been thinking about a new method of ship design. I got the idea from a discussion on the official forums, where I concluded that two similarly sized fleets, each with a decent amount of armor and point defense, would likely run out of missiles before they could completely destroy the other. At which point it becomes a contest of speed and beam weapon range.
That left me thinking, what about detachable missile sections? Sort of a modification of the modular ships idea, but using the fact that once you're out of missiles all of those tubes and magazines are just dead weight. Say, one hull would be mostly engine and the rest beam weapons/PD/armor/etc, then a second section would have no engines but missiles tubes (ASM and AMM), magazines, a tractor beam, and whatever else you could offload onto it (maybe most of the fuel storage). When combined, it works out as a mostly missile armed vessel with 1/3rd engine (or whatever your standard is), but once you run the magazines dry you split off the missile section and suddenly your beam warship is much faster than it would normally be.
Of course, the normal disadvantages of modular ships apply; each segment is easier to destroy, and taking out one can cripple the others. And while your beam armed warships would be faster, they'd also be lacking the extra armor and damage absorption they'd have had as a larger, multi-purpose ship. Still, it's an idea I might try playing around with.