Some thoughts about how armies might work, based largely on the system used in War of the Ring
Forget about towns and cities "commanding" a legion. Consider all units left in a province with a city, but no leader, to be a garrison
. A garrison can be no larger than 5* combat units.
This of course limits each player to 4 mobile legions each commanded by a general, but each legion can now contain up to 10 units i.e. 10 cohorts, with perhaps a bigger pool of units including standard and veteran infantry types. This still leaves potentially 24 legions on the board in a six-player game, which seems plenty. As I've said, I think game of less than 4 players should use only half the board.
When moving into combat, the attacker is considered to be attacking the target province, rather than moving in (which he can only do if he wins the battle).
If the province contains a fortification, then before combat, or after any combat round, the defender can decide to retreat into siege; effectively withdrawing into the fortress to gain its defensive advantage (e.g. only 6's score hits vs defenders). The limit of 5 defenders in a garrison remains, so any units over this are lost. Catapults will have some advantage over fortified defenders. Note that, in general, Barbarians do not have siege engines, so they might have the run of rural provinces without being able to take defended cities.
By the way, I think that Romans should be permitted to build a fortification in a province without a city; think of it as a border post or part of a frontier defensive line. They can develop a town within the walls later if they wish.
A siege is not always fought to a finish immediately, so a turn might end with the attacker occupying the province, but the defender still holding out behind the city walls. In this case neither players draws taxes from the province, nor can new units be placed there.
* or perhaps 10 in a major city/capital)?
Suggested new units placement limit:
major city - 5 units
small city/town - 2 units
Ships built off the coastline count towards this limit; the coast must be of a province containing a town/city
Regarding leaders in battle:
I much prefer the WOTR system of leaders having the ability to re-roll failed combat dice, rather than rolling a die of their own.
One big difference is that in WOTR leaders are never captured, they are simply eliminated if their army is destroyed. I'd keep the capture/ransom from classic COTE.
To develop this further; consider each player (6 player game) starts with 4 generals, each of whom can be given command of a legion. I've never been quite happy with the rule that when you eliminate a Caesar (which might have been largely the work of an ally) you get to control his entire remaining pieces. Instead, every time you capture an Eagle (i.e eliminate the last piece of an enemy legion) you get to use that legion's card/number, and get an extra general to command it. In games with fewer players, each might start with extra generals.
6 players x 4 generals = 24 legions
5 players x 5 generals = 25 legions
4 players x 6 generals = 24 legions
Using only half the board (25 provinces)
3 players x 4 generals = 12 legions
2 players x 6 generals = 12 legions
I also favour some system where captured generals might escape from prison, giving their captor an incentive to trade them in. Also, they are not teleported to your capital on capture; a prisoner must be carried around by the victorious army, though he may be taken to a strong fortress for safety, or shipped into exile on a remote island (which would drastically reduce his chances of escape).