Heres (a few of!) my suggestions I could go on all day, but then noone would read it!

(A) I think the number of units should be increased slightly, but not much (maybe 20-25), but I would make the weaker 'barbarian' type units larger. This is because at the moment a small high tech army can slaughter an enormous low tech army with hardly any losses because the low tech army can only bring approximately the same number of men to the field at the same time due to the way reinforcements are handled. eg double the size of peasant, fanatics, slavs etc so they can 'swarm' the high tech guys.

(B) I think the building time for structures should be proportional to the size/population of the settlement. Its ridiculous that a tiny outpost fort builds at the same rate as your capital with hundreds of thousands of workers.

(C) I think generals should be trained at a military accademy (which you can send your princes to if you want) and this coupled with genetic inheritance decided how good a general they are. The current system which relies on the kings influence is too biased
When a general dies you should have to substitute a new one - not a guy with identical stats appearing - this is totally unrealistic. Great leaders DID die and their countries were often much worse off because of it, but hey thats life!

(D) I want to see a score system which gives me more satisfaction than that end sequence and a high score table. This could be something like GA balancing military and civilian goals, but which gives you a score for the game even if you finish before the end!

(E) There should be more specialisation for which provinces can build which units etc - less generic armies and more reason to contest certain provinces. eg anyone can build tribizond archers, but only in trebizond etc. I think this would show the fact that when a nation conquors a region then the culture of that region can become assimilated into their own (rather than lost forever as it is at the moment - except reemergences)

(F) I like the movement, sea movement and trading concepts in RTW, with a bit of modification they could work well (the one thing I dont like as a result of this is all the siege battles)

(G) Diplomacy needs improved greatly - I want to fight alongside allies on purpose, not by random chance. Be able to trade/give units, provinces, gold to each other. Right of passage agreements. Mutual protection pacts, alliances etc.

(H) Some sort of limit on strategic agents - they can be greatly abused and I've mostly stopped using them as I prefer a battle dominated game. My suggestions would be a maintainance cost for them or each building can support a certain number (eg each church has 2 missionary priests, you get 1 cardinal for your cathedral, 2 spies for each brothel etc)

(I) Archers allowed on the walls instead of infinite tower arrows in siege defences. Suggest the archers have to make a trip to the armoury to restock arrows after they have shot them all - running out as easily as in foreign campaigns would be unrealistic.

(J) You should be able to take the metal armour off in the desert! Just because you equip a guy with the best plate armour in the world it doesnt mean he has to wear it for every fight!

(K) Add momentum to charges, particularly cavalry. I'm fed up with heavy cavalry charges getting stopped by a few guys in a depleted unit or routers. I'm not saying they have to be killed immediately, just that they shouldnt halt the charge the riders who dont connect keep going

(L) Add weapon lengths so eg pikemen have a very large advantage when a swordsman is at the end of the pike, but a disadvantage when (if!) he reaches the guy face to face