I'm really loving this mod. I realized after about a week of playing Vanilla M2TW that in order to have any fun in the game at all, I was going to have to force myself to expand very slowly to give the AI a chance to build up its armies and economy so that I wasn't running over their armies with Chivalrics while they were still fielding mailed knights. The mechanics of PDER are perfect for slowing down the pace of play so the player can't get the steamroller going that completely upends the game.
Still, here are my suggestions on the mod:
(1) I love the AoR system - it's very cool, flavorful, and historically accurate for my distant colonies to field mixed armies of my own culture's units and auxiliaries recruited from the natives. Still, I've noticed that the AoR system can create some pretty serious balance issues, namely, the "native" troops available from the very low-level auxiliary barracks building are often very, very good. This is particularly a problem when playing a faction that doesn't have access to particularly good infantry. I find that playing as Portugal, for example, the Lamtuna Spearmen in North Africa and the Saracen Militia in the Middle East are far better than any spearmen I could recruit in my core cultural buildings (granted, they're not as good as Almughavars, but they have the higher anti-cav bonus and higher unit size, which makes them better for spearmen duties of clogging up siege defense chokepoints). The Saracens even count as Militia for free upkeep in cities. I find that in those regions, I don't even bother to build up higher levels of barracks as there's nothing better to be had. On Iberia itself, the AoR Andalusian Cavalry are also better than the Jinetes - the two have identical stats but the Andalusian unit comes in a larger unit size, at least in Kingdoms edition.
On the other hand, a "nerf" of the AoR units might lose some the current cool mix-and-match armies, and to be honest, I'm not sure if I could handle having to climb very high up the build tree to access good units - in PDER I barely have the cash to keep construction going on basic economic and growth buildings, to say nothing of spending on luxuries like better barracks. It's a nice change of pace from vanilla where I'm rolling in cash by turn 20.
(2) The missions haven't been adjusted for the slower pace of the PDER campaign in general. Most egregious is the papal "build a church within 5 turns" missions, which are an order of magnitude more difficult now that build times are generally 6+ turns, and for me have almost always been impossible without abandoning and wasting existing construction projects. The mission deadlines should be adjusted to reflect the longer build times. To a lesser extent I think this is true of most of the missions with deadlines. "Take X province in 15 turns" is substantially harder in PDER as you can't blitz the province like you could in vanilla. This is true even of opening game rebel province missions, as rebels have been beefed up so much.
(3) The "slightly crooked" merchant traits check for the absence town hall buildings. It seems like the game isn't currently smart enough to recognize the royal hall building line as a town hall analogue. I know I've gotten "crooked" merchants out of settlements with civic centers. Not a huge deal, as it just means a slightly lower mean merchant starting skill, but it nerfs merchants and trade a little bit.
(4) I know you just imported your trait system from the BBB mod, but it annoys me to no end that my game is now capable of _tracking_ which characters are in the royal bloodline, yet when the time comes hands the crown to an usurper anyway.
(5) Again, I know this is something you probably imported from elsewhere, but the more active rebels have the stupid habit of emptying out their settlements and sending out armies to do nothing. Easy landgrab for me!
(6) I've actually seen the tiny islands of Corfu and Lesbos get completely clogged up by rebel armies occupying every single tile. It can be funny to watch the AI drive itself nuts surrounding those places with marine armies with nowhere to disembark.
(7) America kind of sucks right now. I know you're thinking of taking it out altogether, which is a shame, because I always had fun invading America in vanilla. Something about beating down those fullstack Aztecs... maybe you could give the America map the same treatment you gave Eurasia? More settlements, etc.
Overall though, I'm loving it. Thanks for a great mod, it really revitalized my interest in M2TW.