Hello guys! I'm here to offer you a couple of humble suggestions about Great Generals (GGs)/Great Commanders (GCs). First and foremost, I'm sorry for the oncoming long text! I'll try to expose my ideas on the shortest way possible.
In my experience with AND2 (since it's first versions), I've observed that A.I. used to employ GCs in their armies, specially to defend cities. However, in the most recent versions of this mod, A.I. behavior has changed: it now prefers to employ all GGs as Great Specialists in one of their cities (the "military focused city"), instead of turning (at least one of) them into unit-attached GGs or GCs.
As to GGs themselves, I've never seen A.I. attaching them to their units (in old and recent versions of AND2 as well), which seems to be a tendency shared with some other Civ4 mods (like History Rewritten and Realism Invictus).
Such predicted A.I. behavior about GGs/GCs takes away most of the fun and the tactical potential related to the use of these units, because us players are the only ones who (sometimes) use GGs/GCs in combat at all. In particular, the employment of GCs shifts the balance of war in players favor, since A.I. does not use GCs nor seems to understand their power when they wage war against us.
One last problem with AND2 GGs is the method used for their naming. This mod still keeps Civ4 aleatory naming system for GGs (and other GPs), which most of times causes a cultural and historical disparity between a civ and its Generals.
For the reasons exposed above, I propose the following suggestions to AND2 modders:
1. GGs naming system based on the civ where it emerges. It was a feature successfully applied on Realism Invictus mod and it seems to be an easy change (although I'm fully ignorant about programing).
2. GGs that could be freely attached and dettached from units. This feature can be seen in mods like Fall From Heaven 2 and History of Three Kingdoms. The idea of a General forever chained in a military unit is odd and restricts the tactical value of GGs (and the fun in using them as well). Such change in GGs could include give them (some or all of) GCs promotions, in order to confer GGs a real tactical value (instead of only offer small benefits to the unit attached to them). Obviously, this suggestion includes the elimination of GCs as individual and unattachable units.
3. Limit the number of units benefited by GGs/GCs bonuses. Considering the application of our 2nd suggestion, I think we should also restrict the quantity of units that a GG can affect on a tile, based on GGs experience. To determine which units shall be affected, a system similar with the "Hero Units" from History of Three Kingdoms could be used: a GG can attach itself with one or more units at a time, based on GGs experience, and its bonuses are only applied to those units. This feature limits the power of GGs and also increases its tactical value. GGs experience could be determined, obviously, by the number of battles won by the armies they command, and they should require more experience to grow that current GCs (or a system of Dynamic XP could be applied to them as well).
4. Capturable GGs. In AND2 and most of other mods, when GGs are directly attacked by a unit, they simply disappear. I think that GGs should be capturable and employeable by enemy civs (for a cost based on its experience, of course

), as well as used as currency for money or techs in exchange for its liberation. Again, I cite History of Three Kingdoms as a mod where some of these features were implemented and a possible source of inspiration for you.
5. Forbid GGs transformation into Great Specialists as a game option. In order to force the A.I. to use GGs as units, their transformation into GSs could be forbidden (as a game option and not as a fixed feature). This feature would fit perfectly with the last three suggestions presented above.
I hope that these suggestions can be taken seriously and, at least, partially implemented by AND2 modders in the future, considering that (in my humble opinion) GGs/GCs are one of the Achilles heels of this mod (which is fantastic in most of its aspects).
Thank you for your attention!
