Has the potential for adding new strategies and twists to the game
Yes, you know what that strategy is? "Beat this stack of 10,000 ships now, sucker!" Moreover, while it is true that the people in high-level government offices are rarely directly involved in the logistical side of how you're actually going to organize and support a fleet of 7000 ships carrying 160,000 invasion troops off the coast of Normandy and land as much of that as possible in the shortest reasonable time frame, their ability to do a great many things is directly impacted by how well the nation's military planners can manage these kinds of feats. If I'm the President of the United States and I ask the army to fight a war on the Moon using a million men, it does not matter how much I want them to do it, there just isn't at present any technology, planning, or infrastructure in place to support anything like that kind of operation. Given that the game's species are more or less just starting to have access to long-range space travel independent of fixed jump gates, it isn't unreasonable to me that the game's species are not at present capable of fielding as many ships as they want wherever they want them.
You are not going to see any species just jump into space complete with a logistical organization that can support arbitrarily large fleets of ships wherever you want those ships to be. Several of the older spacefaring species might have some slight advantages in this respect, but it would appear that stargate travel was, for all practical purposes, essentially a slow rail network. You couldn't resupply on the way, you couldn't divert to account for changing circumstances, and you couldn't easily extend your logistical network beyond the systems where the stargates were built.
There are probably more realistic ways to represent the logistical issues involved in maintaining a fleet 30 move actions from the nearest base than the logistical limit given by the game, and there are probably more realistic ways to represent the command and control issues of fighting a space battle than the logistical limit, but on the whole there isn't much reason to change it, especially since such changes would most likely cause communications issues between the game and the user.
More closely relates to real Command & Control at the extremely high command level the player operates at, i.e, God/king/dictator/big-kahuna. (Yes I know its a SF game, but unnecessary divergences from reality kill the story.) My random example was the Spanish Armada where in 1588 they sailed a fleet of 130 ships. There are other countless historical examples of large groups of ships, aircraft, soldiers, tanks moving and fighting as a unified force. The current limitations are an apparently arbitrary number pulled out of thin air and having to devote my civilization's ENTIRE research ability to add a handful more ships to a fleet just doesn't make any sense.
And yet none of these are possible simply by the ruler's command. Modern armies have enormous logistical tails, and even historical 'live off the land' invading armies often required some degree of logistical support even if all that that support entailed was replacement troops. Modern-day navies also have higher logistical requirements than most historical fleets despite size disparities; a single US Navy aircraft carrier carries a similar number of people and requires significantly logistical support than went into the (failed) Athenian invasion of Sicily during the Peloponesian war. The ability of a state's military to manage logistical concerns has an enormous impact on that state's ability to project power; one part of the logistical question is organizing the fleets into units you can support while keeping the fleet manageable in battle, another part is getting the supplies to the point of use, and another part is organizing the supply side efficiently. No one, or at least no human living on Earth, has yet attempted to support fleets and armies at the distances involved in a typical game of Galactic Civilizations II, and it is entirely reasonable for there to be issues with the logistical side of things (especially given how recently the species really became capable of interstellar travel without the aid of the stargates), especially given the scale of the ships, crews, and armies involved at later points in the game.
More importantly, playability is improved by reducing the number of commands and clicking around the player needs to do to accomplish a particular goal.
This is the only one of your points that I would not dispute. However, I will counter by saying that there is a gameplay issue in allowing the creation of arbitrarily large fleets - namely, that such fleets create an extremely unstable balance of power. If a single fleet contains a quarter of my military power and it loses to someone else's fleet of similar strength (both in the fraction of their military strength and in comparison to my fleet) and only kills half of it, that's an enormous blow to my military power. Worse, allowing the creation of such large fleets means that if and when I establish a dominant fleet presence in the area it becomes much more difficult to dislodge me or even whittle down my advantage, as you're either stuck sending ships at me piecemeal to get off a few shots before being blown up or waiting 10, 15, 20 turns to build up a fleet that actually has a chance against the fleet I brought into play while I do whatever I want to do in the area and bring in my own reinforcements to further bolster my dominance. At least in GCII you actually stand a chance of being able to dislodge me through attrition even if you cannot defeat me outright, as it's rather unlikely for the relatively small GCII fleets to be able to completely destroy an opposing vessel or fleet without taking damage.