Firstly, the stuff I don't like:
When it comes to combat, Civ is supposed to be a Macro system, not a Micro system. Hence the fact that combat is so simplified. At the level Civ takes place at, each unit can easily be considered to be a Battalion or larger formation (depending on the time setting, obviously), and at this point, a unit's equipment has very little impact on the game - well, up to the time they try using pre-gunpowder weapons against AFVs anyhow

, and that can be dealt with by making later tech units far harder than they are at the moment.
Logistics - it looks a good idea, but this wouldn't be too important until the gunpowder era as early on it was fairly easy for armies to live off the land. Further, given the length of Game Time that takes place between turns, why wouldn't the unit have cleared off to the nearest base and returned with fresh supplies?
Stamina - given that each turn is at least 1 year in length, I consider this to be an uneccessary stat. The fastest ground units move at only 1 square every 4 months at present, thus giving plenty of time to rest.
Now, the ideas that I think will work, if implemented correctly:
Morale - tricky. It shouldn't have too big an impact on the game, but it should have some. The HoMM series had Morale on a scale of -3 to +3. When Morale was low there was a (small) % chance for the unit to freeze and do nothing for the combat phase (represented by the enemy hitting automatically, regardless of A/D ratio?), but when Morale was high the unit got a % chance of a free turn (additional attack at normal A/D ratio?). Of course, HOMM had far more modifiers than would be in Civ, due to magic items, locations and creature types. Maybe just keep it to +1/won last battle and -1/lost last battle. Being outnumbered should be randomised - is the unit behaving like Private "We're all doomed" Fraser, or are they more like "We're outnumbered. Let's see how many I can take with me!"
WE-GO - reading it leaves me feeling funny, yet I know that it's ultimately the best way to go. It shouldn't require that much work - after all GW have developed a WE-GO tabletop campaign system for Warhammer Fantasy Battle.
Stack Limits - goes without saying really. After all, there's only so much room on each of these squares!
ZoE/ZoC - I can see these being important. Also important for the WE-GO system is who gets priority (i.e. who moves first?)? There will be a time when a unit attemts to move onto another unit. There will also be a time when 2 units attempt to move onto the same square. Simple to solve though - assign priority as follows:
1)The player who controls the target square.
2)An ally of the player who controls the target square.
3)Randomised.
Of course, this may not always be necessary, e.g an player attempting to move onto a square under an ally/neutral that has moved should through up an option box of "Is this an attack move?" - if it isn't an attack move then priority doesn't matter.
[edit] - oh, and also a rule that GW called "Don't Pass in the Night", can't remember what that was all about, will have to look it up again some time.[/edit]
Engagements - yeah, I can see different scales of enagements. This is a tricky one though, as depending on the mechanics, a player weak in tech but strong in numbers could use this to smash a player that is strong in tech but weak in numbers.
@Sir_Schwick
I too am trying to figure out why complex = RTS. The most complex game I have ever played (mechanics-wise) is the freeware Steel Panthers:World at War, by Matrix Games which is a TBS.
RTS games tend to be "This weapon does Apts of damage. This unit has B-type armour which reduced damage from that weapon by B, meaning that the shot you fired has taken Cpts of damage away from it."
SP:W@W, by contrast is "OK, You've fired a 17lb. HVAP shell at that Panther. The to hit chance is A%. The angle of incidence is B, which means that there is a C chance of a riccochet. The range is D, which means that the penetration is E+F. You have a G chance of causing serious damage to the tank".
@GeneralX
Nice H2G2 reference. And to further the references of outnumbered armies winning, pretty much any battle involving Wellington.