For Sins of a Solar Empire to become a good implementation of a 4X game and not just an RTS borrowing some surface elements of 4X strategy, it needs a few main things.
I'll try and keep this concise, but pretty much the main element to 4X is making YOUR empire(or directing your flavor of government), not simply controlling a pre-made race and fighting someone else's battles for them.
To this end, I hope that the real mod tools have some damn good flexibilty to them, and perhaps even future patches will add some of these elements.
To me, sins lacks any real definition in alot of its 4X aspects. Weaponry, for example. Weapons are not clearly better than others, and that boggles the mind. Why is a crappy visible spectrum laser capable of the same kind of damage a hard-rad laser inflicts? Why is a laser's damage even in the same category of damage as a heavy metal slug accelerated to near lightspeed? And we're not even into exotic weaponry yet. There is huge room for expansion here.
Customization:
In my opinion, this is litterally the single most important element.
Ships - Being able to make your own ships, to choose between swarms of tiny, specialized strike forces or massive do-it-all monitors, assault ships with banks of furious energy weapons or missle ships that can deploy waves of rolling armageddon, marine vessels that fire off boarding parties to capture enemy vessels and are armored to survive to sherphard those vessels home or raiding vessels that inudate your enemie's ships with lethal levels of radiation.
The direction and tactics of your fleet should be yours to command, and it should be total.
With a bit of tweaking, you could have overall design philosophys for your races, and general looks for ship classes with their individual looks being dynamically based off their charecteristics. A lightly armored carrier designed to hold a small strike force would be a mobile hangar bay, a massive capital carrier would be riddled with hangars to deploy strike forces into the heart of enemy fleets, covered in blast doors to protect the delicate innards that rearm and repair those selfsame strike forces, and studded with massive weapons to discourage those who would dare harm its precious cargo.
Planets - Planets just need more that can be done to them, be it construction of various buildings on their surface, to more orbital structures that do everthing from collect the solar wind, to giant energy-to-matter converter farms that are powered by unfathomably destructive energies, energies that make antimatter-matter reactions look like a child's toys.
Templates or build philosophy's based on planet type, your relative tech level, point in the game, and so on. If you need a fortress world to defend a choke point, or a factory planet, they should all be possible.
Research:
This should be your main route to doing nearly everything else, and it needs an overhaul. A major overhaul. I can't even begin to tackle the things wrong with the system if its aiming for being a real 4X tree, but my best recomendation would be to get it as close as possible to the Master of Orion style, far and away the best and deepest research system to ever be implemented in a game.
New technologies should obsolete earlier ones, be it the equivalent of wheelocks replacing matchlocks, cartridge ammunition, rifling, computer chips and software versus abacus, and so on.
And for those epic games, the ones that may span days, their should be a point to research too, be it Kinetics XVIII that makes your ships cheaper to build, your weapons slightly more effective, etc. Something that you can still pour effort into, such that a small fleet of super advanced ships don't lose to someone armed with the equivalent of paintball guns in space. (I.e. conventional weaponry being completely inefective because the target ship phases in and out of phase space, traveling at superluminal speeds and existing for femtoseconds at a time, not letting in any part of the EM spectrum useful for weaponry, and completely bypassing the effects of physical objects, not existing for long enough to interact with them)
Diplomacy:
What can I say? It's hugely limited in scope. Degrees of economic alliances, superior or inferior trade agreements, gifts and demands, research pacts, etc, there's more that can be done, both for human and AI players.
Control:
There simply needs to be more of this.
Frankly, I'm not really sure at all of how one would keep the current system of capital ships, but one could easily modify it to a crew system that would transfer over to new ship types, or continual overhaul of older ships till there's not a part amongst it that's original.
With new research and modification, new abilities become available and obsolote ones are scraped. New systems come online, and while crew familiarity with these new fangled toys may not be the same, they're a damn good crew, and they'll figure it out soon enough, but while they're at it, it's still a vastly superior system, they just have yet to figure out how to ring out of it as much as their previous stuff.
Real time slider bars for your planets let you scale up or down their goals, be it economic early game so you can grab all you can, research so you can tech up to defeat those annoying swarms (a few warheads armed with antimatter munitions in the middle of those million tonne frigates, seperated from naked space by titanium alloy and first generation plasma shielding, and the results are sure to be interesting) or man those factory's to start pumping out ships, or perhaps cover your planet in indirect and direct fire stations (Missles and lasers).
I'll edit this later as new ideas and suggestions come to mind, if anyone appreciates this post. I myself do not have the skill to make a TC for SOASE, even if the mod tools came out with the robustness to get the engine to do 3-point mid-air flips.