This is intended to be a discussion of faction customization costs and how to improve on the current system. Before I begin, I would like to point out that the 0 point "picks" are something I really enjoy. Things that change the game flavor, but not in an imbalanced way (except for Heroic which is an oversight, I'm sure). Also, the upgraded Archers, Axes, etc lines are also thematically interesting to me, although I haven't gotten very far into a balance analysis of combat weaponry (and upgraded weaponry perks) yet.
The cost/benefit ratio of the various Faction Customization abilities is not very well equalized currently. This is largely due to the small amount of granularity you have because of the design choice to give 3 points and make most things 0, 1, or 2 points. What I recommend is increasing Faction Customization picks by a significant margin and balance this by increasing Faction Customization picks costs. If you raised Picks to 30 from 3, and raised cost by a factor of 10 as well, there would be effectively NO CHANGE. However, the advantage this provides us is this: We can now provide a smaller step change when assessing the cost/benefit ratio of a given ability. This is something that can be done with minimal effort in a small time commitment (F3 "cost" in CoreAbilities.xml, add a 0, F3, edit, edit, done). Once things have been raised by a factor of 10 or whatever you choose, it will allow the various faction customization options to be more finely adjusted to equalize the cost/benefit ratios. Before anyone goes down the "just mod it yourself" path, I have (mostly, except for split outs), and my intent is to help improve the BASE game via positive, constructive, concrete feedback.
My specific recommendations are:
ALL of the "you get 1 tier one technology" faction customization picks are pretty underwhelming compared to the % faction bonus abilities. There are more exciting ways to go about this. For example, a 1 point cost pick that unlocks worgs. The player still has to find and build a kennel, and/or save the gold to buy a champion a worg, but it's an interesting option compared to "I've skipped 6 turns of research". woo. hoo. Or a partial unlock bonus from a higher tier, such as "Firestaves" which unlocks the 6 attack power ranged weapons from the start for 2 points, etc. Again, they still need to get the crystal to make a unit wielding them, and/or save the gold to buy one from the Shop.
Defensive is 20% per city level in my modded version. It's just not compelling at 10%. I'm not even sure if it's compelling at 20%, but it makes Krax a tougher nut to crack.
Split out the Enchanters ability (see above for gear unlocks you buy), and just make the Scrying Pool it's own pick. Trust me, no one is picking it for the staves. In my higher granularity example, the Scrying Pool would be one of the more expensive picks.
Lower the % bonus for Lucky, and split this out from accuracy. This also reduces the plausibility of a major abuse path for dodge stacking.
By increasing the granularity, MANY of the multiple ability picks could be split up. Providing increased variety and customization options. Great examples of this are the Decalon, Death Worship, and Fleshbound Tome.
For example, instead of Having the Decalon cost 4 points in a 12 point system, it could be 4 different one point picks for the same relative cost as the current system, and also provide more customization.
MasterScouting should CLEARLY be costing more than 1 pick in the current system, it is very powerful from an early expansion AND strategic mobility point of view. It is powerful from the start of the game until the map is covered in roads and teleportation is trivial, i.e. late into the game. Personally, I would recommend splitting this into subcategory bonuses which are each picked separately.
To summarize, costs and/or faction customization benefits need to be better balanced. This can be done by increasing granularity (raising picks AND costs) and splitting up bundled options to make the cost/benefit ratio of the various faction customization picks better equalized and provide deeper customization and thematic choice for players. The cost ratio increase can be done in a few minutes (see F3 above), the splitting up of picks would be largely cut and paste. It's the getting a whiteboard/notebook/spreadsheet/forehead tattoo of what the final costs need to be that takes some time. And the work required to format the syntax for adding completely new ones.
You could up-ratio the current system, and split out the bundled faction customization picks in a free patch. Then, given a better (more granular) framework, create a deeper faction customization / sovereign customization to include in your next DLC for nonmodders. More added value for the customer at a minimum of developer time investment. Win, win. Think about it.