My personal preference seems to hint towards using Civ IV as a basis, simply because a lot of the issues I have with Civ V seem to be intricately part of the engine for Civ V.
I have the following key gripes with Civ V so far (I will add to the list as I explore more of the game):
1UPT: This simply doesn't seem to work as was intended, and is the biggest issue that I can find so far. While it does increase the tactical aspects of combat, it messes up unit routing significantly, since units are either forced to wait or detour around units of the same type (military or non-military). Such detours can be disasterous, and can only be avoided by immense micromanagement of units at the tactical level.
The following incidents are all stemming from 1UPT and routing issues:
- Military units taking to embarking to detour around another unit, only to be defeated while unprotected in the water*.
- Military units detouring around units, leaving civilian units like settlers exposed*.
- Military units detouring through City State territory, angering City States needlessly*.
- Civilian units detouring around workers constructing improvements*.
- Workers having Route To orders interrupted by other civilians*.
All of these can be fixed by resolving other issues, but they are ultimately caused by the 1UPT mechanic interacting with other mechanics negatively in Civ V. Alternatively, removing the 1UPT restriction is a possible solution.
Embarking: I can understand the point between embarking, but the main issue with embarking is that it effectively turns water tiles into land tiles for routing purposes, with little or no regard to the fact that most units are defenseless when embarked. As such, all units are inclined to embark and sail around the coastline when given the option. This occurs even when the issues with 1UPT aren't included. Ultimately, the benefits of embarking are lost because of the increased micromanagement due to the routing issues involved in dealing with the coastline.
The easiest solution here is to simply allow embarked units to defend. This doesn't really deal with the routing issues, but it does mean that the units are less vulnerable when they embark, so that you don't lose units to what is essentially an AI error.
Escorting and Armies: With 1UPT, the ability to create armies by combining military units has gone. While this increases the tactical aspects of combat, it makes for a logistical nightmare, since weaker units cannot be as easily protected without taking up a lot of space. Moving an army is tedious, especially when moving through choke points.
An additional consequence of this is that the ability to escort civilian units has also been removed. As such, units like Settlers are particularly vulnerable when travelling, simply because their military escort might take a different route. Plus, should the military escort be interrupted, the Settler will often continue exposed through a warzone, typically leading to their capture.
I don't know of an easy solution to this, since it is a compounding factor of routing issues and 1UPT that simply makes this a logistical nightmare to handle. I think that allowing civilians to defend might be a start, making them less vulnerable. An alternative might be to allow military units to transport civilians (in a similar way to how missiles can be transported, perhaps) so that they stay with the military unit.
This idea could be expanded - perhaps certain military units can be transported by other military units to create armies. For example, ranged units might be able to be transported by melee units, and naval units can transport land units. Thus, the units that you want to defend can be visible, while the protected units are transported.
City-States: City States are great, and are basically like mini civs with their own lands and agendas. Unfortunately, City-States are not treated like civs when it comes to routing, and units will continually route through them without regard to whether or not this will damage any relationship with them.
A solution to this is to treat them as Civs. In fact, the simplest option doesn't actually need a mod at all - you simply remove all the City States and replace them as Civs. However, this does mean that a lot of the City-State based mechanics become largely redundant.
The ideal solution therefore is to have City State territory treated like Civ territory. Units won't route through it unless their borders are open. Being friends with the City State automatically opens their borders - you don't have to negotiate this. You can still spend gold to become friends with a City State and have them open their border.