HO BOY, SUGGESTIONS TIME. Note that while this is made with 4.0 in mind, it's still applicable to 3.x.
Merchandise
One thing that's been bugging me more and more with PoP is how much useless merchandise there is to be had- I often find myself wandering around from town to town, traveling the whole world in a cycle multiple times until I find decent equipment. There's so much useless equipment that's made obsolete by much, much better equipment. I'm not talking about something that requires 11 Strength vs 12 Strength- I'm talking about two items that have the exact same requirements, but one is better in literally every single way. Even worse if there's equipment with HIGHER strength requirements, and is still worse is basically every single way.
I propose simply removing these less-than-useful goods from the merchandise list. I'm fine with having "obsolete" equips for troops and NPC's- but it really makes it annoying when you're going from town to town and keep getting really crappy shields, armor, and etc.
Please note I'm not saying "remove the crude/cracked/not-lordly/not-masterwork equips!". Just the ones that have base stats inferior to other equipment in the same bar (as in, equips that require the same exact things- such as armor and weapons with the same strength requirements).
Crossbows
Please, PLEASE make crossbows have better accuracy. Not a whole lot- but man, they pretty much suck at any range except 10 feet or closer. If it's not too much to ask, it'd also be nice to have Mettenheim arbalests be available for purchase. Dedicating to using crossbows on a character is painfully bad in PoP (without editing item values, anyway).
Selling Cattle
It'd be udderly fantastic if you could sell cattle somehow- it's annoying to raid a village, then be stuck with effectively useless cattle. So you just abandon them there (or slaughter them for really cheap beef that hardly nets you much profit anyway).
Raiding Villages
Maybe I'm just a baby, but it's EXTREMELY annoying that you can't cancel raiding a village. I'd be okay with it if NPC lords couldn't, but... they can. So you'll have crappy little lords with 20 men raiding your villages and running away, but if you have 100+ men raiding a village you're suddenly greeted by the enemy's entire friggin army and just have to take it.
I know it's more of a thing with Mount & Blade itself than PoP, but it'd still be great if this could be rectified. It'd be really cool if it actually required a certain level in tactics, too- like, you need (or someone in your party needs) level 5 or 6 tactics before you can cancel a raid.
...unless I'm really dumb and there already is a way, but AFAIK you can't.
Noldor Victory Requirement
As suggested earlier in the thread, allying with the Noldor (should they be in 4.0) should be optional. I would prefer it so there's a choice between either crushing their armies entirely, or allying with them.
Trade Goods Prefixes
A neat feature of Floris- this made trading a lot more interesting. It's nice to have cheaper foods if you're low on cash, and also nice to have finer foods if you have the dosh to throw around and want to keep morale high. In general, it makes trading a lot more interesting, too.
Hiring "Bad guys"
It'd be really, really cool if you could hire certain typically un-recruitable if you meet certain conditions. For example, to hire heretics and lead a heretic army, you'd need positive relations with the heretics. For all of them, you should need a negative honor rating. Probably not particularly lore friendly- but that's kinda the point of an open world game, no?
Keep in mind, I'm not suggesting making it possible to hire on demonic magni or the like- just easier access to certain troops without having to recruit them via rescued prisoners only.