Well, one question that needs to be answered first is scale. Is this going to be MoO2 scale, where 20 ships is a huge fleet and is a chore to play with, or are we going MoO1 where hundreds of ships per side in a battle is not a rare occurance. I hope very much its MoO1 scale...
Assuming a MoO1 scale, and appropriately designed combat (stacks or groups to simplify command), small ships can very easily be made useful just through accuracy modifiers and sheer numbers.
As for weapons, I agree that mere quality increases should just be used. However, there can certainly be a range of different effects. For example:
c-Beam Weapons (Lightspeed beams, Lasers)
sub-c-Beam Weapons (sub-Lightspeed beams, Ion Cannon)
Projectile Cannon (Physical Projectiles, Mass Drivers)
Missiles (Big stand-off range weapons, Nuclear Missiles)
Rockets (Close in, only slightly guided mini-missiles, Merculite Rockets)
Torpedoes (Energy Spheres, Plasma Torpedoes)
Defensive Strike Craft (Ships who attempt to shoot down incoming fire, Laser Fighters)
Offensive Strike Craft (Ships that blow larger ships up, Plasma Bombers
Bombs (Surface/Stationary removal, Anti-Matter Bombs)
Exotic-Tactical (Special weapons for battle, Energy Pulsar)
Exotic-Strategical (Special weapons for out of battle, Seismic Inducer [Planetkiller])
Even if all weapon tech does is get better in those realms, there would still be quite a variety to combat. And then if there is distinctions in those groups, say Tachyon Cannon have a huge accuracy and range boost but the older Bomb-pumped-Xasers do more damage, the strategies in design are limitless.
Personally, I'm for a deeply involved ship-design system. Like, Involved to the point of working with magazine size for my missile launchers, and the amount of armor over them. However, for those who don't like that kind of complexity, a simplification system that would cover all the niggling details and just require the components you want to be added would be nice.
As for the Ubership concern, if the tech tree has some randomization and choice, ala MoO1, designing an Ubership for a 'Given Tech Level' will be hard if no concrete tech levels exist. Do I commit to designing my new Archangel Dreadnoughts now, or do I wait until I get Tachyon Cannon? And if I wait for Tachyon Cannon, should I wait the little bit more for Subspace Drives? And then should I wait for the Oracle Algorithim? etc.
Someone made a comment on Refinement being its own research. The thing that I saw that lead to in MoO3 was research really meaning very little, as most of it is just tiny improvements. But when you got Ion Cannon in MoO 1 over your starting Lasers, you noticed.
Well, I ranted for a bit more than I meant to
, I'll just end it here...
Edit: Well, not really. Was redirected here from another post about upgrades. Heres my view on that.
A ship built 200 years ago should not be able to compete with a modern warship period, no matter what you do to it, short of deconstructing the entire thing and building a new ship in its place. Think about the U.S.S. Constitution. It cannot be upgraded to the modern standard of naval warfare. I see no reason whay equally ancient starships should be able to accomplish a similar feat.
So how should upgrades work? Upgrades should merely be replacing lower quality items that are the same with better ones. This does not mean replacing replacing Ion Cannon with Neutron Cannon, it means replacing Ion Cannon with better Ion Cannon. Sure, you could replace them with Neutron Cannon, but that would mean tearing the entire ship open, ripping out the Ion Cannon themselves, the charged particle acceleratiors, the ion tanks, the charged targeting matrix, etc. and replacing them with the Neutron Cannon and equivalent structures. Much harder than taking out a mag-array and a few other components and replacing them. Thats just routine maintainance. The huge ripping and tearing operation on an old ship might save you 10% of the newer ships cost. But if I pay the extra 10%, I have a new ship and an older one that still can fight. Guess who wins between 10 Level 5 ships vs. 9 Level 5 and 9 Level 4 ships.
So what if you have a fleet of battlecruisers using Tachyon Cannon when you get Subspace Disrupters? Then you keep on using the Tachyon-equiped ships, declare the class obsolete, assign them to border systems where their deficencies wont matter as much (or keep them with the main fleet as fodder), and design a successor class. What if you just started building Tachyon ships when you got the disrupters? Well, you stop, and build the newer class. And eventually as you are using Quantum Annihilators, the old Tachyon Cannon ships can be turned into high-quality razorblades for several star systems. (i.e. scrapped)
The key thing though is just because a ship falls a few tech levels behind should not mean its useless. Less useful, sure. But still useful.
I rant way too much...