1) Let him report separately about the comparative sizes of air, ground and naval forces (not just total military size like it's now). You should be also able to know the comparative size of your or your coalition forces against several enemies.

2) Let him calculate for you how many troops and how much time is required to quell the resistors efficiently.

3) Let him remind you from time to time that your military forces are becoming outdated compared to most probable enemies (just to automate 1) )

4) There should be some money assigned to automatical upgrading of the troops, let advisor determine which should be upgraded and when (if unit can't be upgraded in a city where it is stationed, it should be rotated with a unit from city where upgrade is possible). This only applies to current upgrading scheme, dunno how it will look like in Civ4. Of course it should be optional, very much the same as city governor.

5) Damaged units that are fortified in cities should be automatically unfortified once they heal themselves completely (not really a Military advisor improvement).

6) It should be Military advisor screen where you command the spies from, not the diplomacy one.

Idea improvement: Allow new number - a player-set amount of gold that will be stored only for military needs(ex. player set 1000 gold limit). That mean at peace you set number so after 20 turns you got 1000 gold filled in military budget and you can't spend it. After 20 turn you gaot a sci-breacthrough and got your(for example) warrior able to upgrade to Spearman. Your Military advisor may be set to: auto-upgrade all sentried units. So that means military budget can manage upgrades and even if city building military structure(barracks or wall) advisor can hurry that construction. Player can define percent of building and upgrading cost(60% of budget to upgrading, 40% - constr hurry)

6) It should be Military advisor screen where you command the spies from, not the diplomacy one.
It is because the diplomat and the spy share the same role in civ3.

Not to mention spying in general is not really a military function.

1) Let him report separately about the comparative sizes of air, ground and naval forces (not just total military size like it's now). You should be also able to know the comparative size of your or your coalition forces against several enemies.

That would be very good, especially, IF the different forces were more balanced.

2) Let him calculate for you how many troops and how much time is required to quell the resistors efficiently.

Would be nice.

3) Let him remind you from time to time that your military forces are becoming outdated compared to most probable enemies (just to automate 1) )

4) There should be some money assigned to automatical upgrading of the troops, let advisor determine which should be upgraded and when (if unit can't be upgraded in a city where it is stationed, it should be rotated with a unit from city where upgrade is possible). This only applies to current upgrading scheme, dunno how it will look like in Civ4. Of course it should be optional, very much the same as city governor.

THis would not work out well. It would leave vital cities weak during an invaision. Make the player control this.

5) Damaged units that are fortified in cities should be automatically unfortified once they heal themselves completely (not really a Military advisor improvement).

This would not work. Also, I believe that Civ is further weakness up recovery units. Not allowing full fortication on the same turn is one example.

6) It should be Military advisor screen where you command the spies from, not the diplomacy one.

I would rather all intelligence was gathered into a single place and run by a single Intelligence Advisor. He would also warn about upcoming possible threats.

Not to mention spying in general is not really a military function.

Spying actually has direct relationship to military and sprouted from that. Even using diplomatic status as a cover, spies still belong to military in nearly all of the countries that use them.

Don't forget, that although KGB is the most famous due to its numerous political actions and its role inside the Warsaw Pact countries, it was GRU (Main Intelligence Directorate of General staff) that performed the bulk of military intelligence operations abroad.

But I agree that it's probably better to introduce a separate Intelligence Advisor, which could also provide you with detailed an information about your own citizen's moods (e.g. warn about upcoming culture flip or anything like this).

The thing I miss the most is being able to upgrade from this screen.

In Civ3 I always right click upgraded my units from the military advisor.

I liked the Civ3 advisor a LOT more and feel this one is somewhat useless. I never use it unless I accidently hit the wrong button and it opens.