I just feel like it would be near impossible to find a your own base if you had to search a 25X25X25 km cube for it. Maybe there can be sub sectors or something that are the saze of a planet. Also, having multiple planets in one sector would cause many problems when trying to load in a base since it would destroy everything in the sector just to add a small object. (refering to the commands import_sector, despawn_sector, export_sector)
The problems with sectors are: only your own and neighbouring are loaded from server, between-sector fights, multiple-sector ships.
I agree on larger sectors, but isn\'t 25 too large? I would suggest 16km (2^4), one planet there and the possibility to see the names of planets on your screen / in your sector.
Maybe finding your home would not be an issue with better map support and custom named-waypoint, named-lists (Faction, MyGroup, Own)...
For weapons, shields, etc..., If you want to give big ones a penalty (and btw improve performance of 1by1 kills), make it disable for sqrt(num-blocks)*x seconds whenever some block of that array got destroyed.
A player seat could be 2x2 on the floor and 2x2x2 \"air\"-blocks above - if the player presses activate, he freezes in this position and has access to surrounding computers, etc, press R twice in a short time to leave.
Hps or heat-sink ability could depend on hulls in an array. Some systems - like hull plates - could work without master. Select one and and assign an equal block to make them a group without master and do some magic on the result depending on x/y/z size, number blocks, etc.
We could have multiple warp strategies - node-to-node (stargate), wormholes where players can fight for a claim on it. FTL-engines for separated combat movements, a slipstreams between close planets and star systems (but you won\'t find ressources aside it if you use it). Slingshot-machines which do not require end-nodes but have a shorter range (mabye 3-5 sectors), etc and let the server admin decide which to enable.
I didn\'t read everything - I am more a fighter-pilot or builder or team player - not a fleet commander who lets AIs fight for the almighty human.
But I like the possiblity to use AI to defend at least the stuff orbiting a homeworld.