One thing I've continually suggested is the following, with logistics being a leader trait, modified by civ techs.
a) Logistics techs increase your logistics limit. Start at 4, +2 per level of logistics tech.
No more building multiple units, 1 unit, 1 person.
c) Certain units cost more then 1 point of logistics, such as monsters
d) Certain heroes get the commander special ability, which increases logistics for their stack
e) Only one stack per square
f) Cities add their 2*city level to logistics
g) Get rid of the 12 units/hex hard cap
h) Certain heroes get leadership special ability, which buffs stats for units they command
i) Heroes add Cha/5 to their logistics limit.
j) Heroes do not count against a stack limit, and hero charisma can be combined to add to a stack. (you can stack of doom if you have enough heroes, which may be needed to take high-level turtle cities outside of sieges- though encouraging sieging would be nice also)
This would make the game much more about ther heroes, which is what I'd want to emphasize. Cannon fodder units would still have use, especially in garrisoning.