Sins of a Solar Empire is one of the best I've played, It's got a good pace to let you keep track of everything that you need to. I actually prefer sci-fi/starship RTS to fantasy, the whole 2D/3D thing doesn't really bother me. Most interstellar astronomy is centered on the galactic disk, so it's not unnatural to think that much of 'traffic control' in a solar system would have a 2D influenced representation. That said, Homeworld had a very strong 3D element to it's interface.
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One of the things I've never seen implemented is some sort of "AI Governor". Essentially something you could set on a per-planet basis that X percentage of the production goes to the empire's coffers, Y percentage goes to local defensive structures and ships (submenu to set options on what structures and ships) and Z percentage to planetary welfare, etc. etc. Basically keep track of all the 'constant grinding bookkeeping issues'. Research is a 'One Time' expense dealt with through imperial coffers, Interplanetary/Interstellar fleets are taken from the Imperial coffers, etc. etc. and are directly controlled by the player. You could 'turn off' the governor on any particular planet (Ie: the Imperium takes direct control of the local situation leaving the local officials as figureheads) and make all that planet's decisions manually.
Make it smart enough to know when there can be no more defensive structures, so it sets structures to 0, but sends it all to ships, when the planet cannot support any more defensive ships it shunts that money to planetary welfare and imperial coffers...
It's always bugged me that when I'm trying to redistribute ships to respond to a pirate/enemy invasion, other planets will finish what they are doing and send me a message about it -while I'm busy!-. And then when the crisis is over I have to browse through my empire to find the planets that finished their tasks (and have been done for the last game-year), meanwhile the computer AI has a ready list of idle planets and factories to redirect with all the processing cycles to do so before the alert message has finished playing on my screen about mine. Apparently with populations of a few billion people, not -one- of those lazy -------- in the local administration can take the initiative to start work on the necessary planetary upgrades, even in the name of "More Jobs".
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Other thing: Imperial Guard. The Sardaukar Guard from Dune and the like. Elite warriors who directly serve the emperor without question, get he best equipment, and are feared inside and out of the empire for their effectiveness. Obviously not something you get to start with, but as part of the sci-tree advancement, then you set some percentage of a percentage of the Imperial Interstellar fleet to get untested prototy...err... 'upgrades' in equipment and brainwash..errr.. 'training'... yeah, that's it, 'upgrades' and 'training'.
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Boarding actions. Homeworld had some good ideas, but most every military ship will have 'some' ability to board another ship. Upon capturing a ship, it's recent travels should clear up the 'fog of war' as its records are analyzed by the capturing vessel. Possibly other effects based on what ind of ship was captured (like an "Enigma Machine" being captured on a command or capital vessel). If a captured vessel can be brought back to a shipyard then the capturing force gets upgrades to the tech tree based on what the ship was equipped with (Not necessarily full upgrades, but a +20% bonus to each tech). If the factions have different tech-trees, then captured ships open the possibility of reverse-engineering other factions tech, so that an empire's tech tree can become a unique set instead of the same tree over and over again.
Of course this means there's actually a need to 'scuttle' ships before they're captured, and to send attack ships to destroy captured vessels before they escape....
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I'd like to see it, but it adds a whole new mechanic to the game (A few games have flirted with the idea, but I've not seen one that really does it well): Detailed planetary invasion and conquest. Again another use for governors is to let the AI handle the piddling details of the empire while the emperor takes direct control of a local situation, or leave the AI ground commanders in charge of deployments. It wouldn't have to be as detailed as starcraft (Actually that level of detail would be detrimental IMO), but having the ability to control the makeup of the 103'rd Imperial Battalion (Ie: overall size, percentages of Infantry, Armor, Mecha, Air Support, Orbital Strike support, training and experience etc.) and determine which planets they are sent to, rather than just sending "Generic Troop Transport" full of generic "army" to fight generic "Planetary Defenses" etc. etc. etc. Obviously this means that there's a "Ground Force" tech tree in addition to the "Space Forces" "Political" and "Economic" ones.
But again this is a big addition to an existing space RTS, so it's more wild-wish-list than the others.
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Anyway, My RTS wish-list.
$0.02.