Okay, before I get too lost in my own thoughts, I figured it would be best to take all the civilizations in this mod and break them down into groups. The first group is that of the civilizations that I feel lack a distinct play style, and thus should have some fairly significant changes to bring them up to par.
So far, I have the following down as need significant work: Amurites, Hippus, Lanun, Luchirp, Malakim, Elohim, and Mechanos. In the case of Amurites, Hippus, Lanun, and Mechanos I believe the problem could be solved by retooling specific unit lines. In the case of Amurites, either an assortment of UU casters, or as a mod I just read about did, some new spells that only they have access to. For the Hippus I think that they should either receive a line of UU mounted units or become more focused on mercenary recruitment. For the Lanun, UU naval units or more hybrid land-water units (like the war turtle). For the Mechanos, as you already stated replacing their archery line with an assortment of gunpowder units would be fine. What to do with the Malakim and Elohim, I have no idea, but I'll keep thinking about it.
Additionally I just want to say, if anyone disagrees with my categorization of the civs or my opinion on what to do to solve the problem, please give me some feedback. More opinions is always better.
Anyway, next are the civilizations that I believe have a unique feel but could use a touch of flavor, though they do not necessarily need to be totally retooled: Bannor (crusade is nice, but not enough to make them interesting), Clan of Embers (maybe a couple more UU troll/ogre types? or maybe move training yard up a tech level), Doviello (shapeshifting is nice, but I'd like to see more forms available for different uses [stealth form, flight form, etc would be amazing], Grigori, Sidar, Ljosalfar, and Svartalfar. In the case of the elves I feel that they are both interesting and fun (love my builder civs) but are just too similar too each other.
Finally the civilizations I believe are unique enough to not warrant any changes, but might require slight tweaks for balance (or significant tweaks for balance, depending on how the other civilizations are altered): Balseraph, Calabim, Illian, Khazad, Kuriotates, Sheaim, Infernal, and Mercurian. Though Mercurian I am on the fence about, they are so radically different (as are the Infernals), but I don't feel like they do much other than be a sidekick.
edit: in the case of the Sidar I would honestly like to see their assassins lose the stealth and maybe get some more builder-type UBs? I feel like the stealth just forces you to micromanage that much more, and is a bit overpowered. Maybe they should just get a UU that can't attack but has invisibility and decent range of vision. I can imagine if they ever solve the OOS problem, fighting a Sidar player would be super annoying - you'd have to guard every worker you had.
also I would really like to see some of the mastery towers redesigned. Right now they're all pretty mediocre considering the effort involved.. and I'm still a supporter of expanding the tech tree more.. maybe alignment specific technologies. Also, I think slavery is a micro-management nightmare.. maybe the capture rate should drop to 10% and the abilities they have should be significantly increased (the ability for all civs to upgrade to infantry would be nice, and Doviello could just get a bonus.. maybe everyone gets -1 strength on upgraded slaves, and they get a bonus +1 strength.