It sounds like you want a completely different game, but there are some decent ideas.
Limiting stack-size would suck, but having a GG increase combat effectiveness and having combined arms bonuses (at least for defense) are good ideas.
This would be a good idea if it were balanced. Could be easily abused if there were too many bonuses.
Why do people want this? This game is not meant to be a strategic military sim.
Pretty much everything else (except eliminating the AP Victory, which everyone, everywhere wants to get rid of) makes it a decidedly different game.
I don't think it makes it a significantly different game. It keeps the core of civ4 while at the same time making combat, espionage, tech trading, and diplomacy deeper and make them more logical.
Combat: Everyone had swordmen, but no one would argue they were all equal at all times. So why are they all equal all the time? Upgrading with techs and techs specifically designed to upgrade units would make them not all the same.
Espionage: Is espionage simply "steal tech, steal money, or 1 turn of anarchy" in real life? No, it's a gross over-simplification (all other missions are essentially window-dressing, as they almost always accomplish nothing). Placing spies in the cities that can be rooted out (while pissing off your citizens with your oppressive anti-spy liberty clamp-downs), that slowly gather information as time goes on and get more an more bonuses for running missions is much more effective. I also should have added that I think they should get a crimea style "flip city" as long as they have been there for 10+ turns (normal speed) with a low chance of success, and a high chance of getting caught and pissing off your neighbours (with failure still resulting in 1 turn of anarchy, so you can swoop in with troops if the spying fails).
Diplomacy: Is the middle east a peaceful love-fest because they are all Islamic? No. Because nations rarely become "friendly" with one another, ever. And when they do, it's because of shared religion, shared government-type and shared war (US, Canada, Britain and France). Only nations as peaceful with one another as that freely trade techs around as much as cautious civs do in civ4.
Tech spread reductions: Lots of technologies are developed without any government oversight, and are not even recognized for what they are. Music and archery predate farming, and were just passed around to everyone without anyone even thinking about the need to protect the technology or trade others for it. That notion of monopolizing and trading technologies didn't even really arise until nationhood. And it's actually mostly being abandoned. Corporations are flocking to China to have their goods made because its cheaper, without even realizing that China is simply taking all of their ideas when they are intellectually robbed and new companies still somehow don't add that into their calculations of profit). I was thinking that free market should have an effect on tech reduction too, as that is a large part of what it does in real life... and in a peaceful world it would be the ideal economy for just that reason.
These are the things I am trying to make more logical and deeper, and I think the reasoning is sound. But feel free to disagree of course. I can already see that espionage might be end up being too micro-management intensive in my system (but civ5 goes way too far the other way, and my system would have a large "fire and forget" capacity of placing spies in cities one time, and I'd put a spy icon on the city to show you have a spy there. A green one if it's yours, a red one if it's an enemy one in your city), and tech cost reduction might have too many variables to get a quick read on what is optimal.
As for Hexes, I only somewhat care about that, as it is a slightly better approximation for movement while still only being an approximation like squares, and spherical maps ios just a "this might be cool" which might actually be really unfun. Certainly, spinning the globe around all the time would be annoying if implemented poorly, so it would have to have something, like the mini-map to make it faster and easier. But I don't know that would be well-represented on a 2d screen. The spherical map would actually be a really bad thing if implemented poorly.