How does the Army Graph look? How often does the AI suffer losses against independents (during the first 5-10 turns, perhaps), and how much does that affect its early game?
If the AI attacks too soon, it could take a while before it gets another army that can tackle level 9 independents. You could try lowering the indep strength to 7 to see how it affects the AI.
Have you looked at Random/SemiRandom yet? It can be used to create custom gods that SemiRandom randomly gives to AI nations. You can change even more things than you can in normal Dominions, making the pretenders start with magic items or experience, probably even spesific units under it's command.
Ballbarian's thread here:
http://forum.shrapnelgames.com/showthread.php?t=34826
Sample GOD file from the same thread. I've added comments, or changed Ballbarian's, when necessary. It can use all # commands listed in the Dom3 MAP-EDITING manual (map-editing and mods are different).
#god 11 138 -- nation 11 is EA Pangaea, unit 138 is Gorgon
@RANDOM comname COMMANDER
-- @commands are commands that SemiRandom can parse some way, that can be used to e.g. give a pretender one of F9, W9 or S9.
#clearmagic
#mag_earth 9
#mag_nature 4
-- pretty much what you expect
#additem "Shield of Gleaming Gold" -- hand slot
#additem "Sword of Sharpness" -- hand slot
#additem "Black Steel Helmet" -- head slot
#additem "Robe of Invulnerability" -- body slot
#additem "Boots of the Messenger" -- feet slot
#additem "Amulet of Antimagic" -- misc slot
#additem "Amulet of Missile Protection" -- misc slot
-- same here
#dominionstr 11 10
-- nation 11 (EA Pangaea) has dominion 10
#scale_chaos 11 3
-- Ea Pangaea has turmoil 3
#scale_lazy 11 1
-- sloth 1
#scale_cold 11 -1
-- heat 1
#scale_death 11 -3
-- growth 3
#scale_unluck 11 -2
-- luck 2
#scale_unmagic 11 2
-- drain 2
The amount of points isn't limited in any way. At most, you'll get a single message at the start of the game telling you that several nations' pretenders are better than they ought to be, but you can still give the AI nations all positive scales and a titan pretender with two magic paths at 9 and three more at level 4. You don't have to use all of these commands, either. The file name follows a format that defines the affected nation, and another .god file might only be used to ensure that EA Pangaea has good dominion and two good scales (Growth and Luck, in this case), in addition to whatever it's randomly given by Dom3.
#dominionstr 11 10
#scale_death 11 -3
#scale_unluck 11 -3