So, I've been playing both Prophecy of Pendor and Floris Mod Extended+Reworked Troop Trees... Up to before I can conquer/acquire a castle/town myself.
Different beasts PoP and Floris.
Convenience: Floris has so much of the little stuff put in that adds up. While PoP, only recently added in the talk to Guild Master button.
Tournament: Floris has an arena style tournament, based on points gained during the match, instead of the Native style tournament. I lurve it, especially comparing it to Native.
Trade: Actually, I personally don't play the trading game. I think there is a food supply thing in case you want to starve out a castle/town in a siege. It takes time to replenish that. Forgot which one has it...
Floris: Has a setting where there is actual supply and demand, for the town workshop investments and land ownership/rentals. You can pick up a Merchant's Ledger, I assume you can use it to record pricing of goods after you spend the time to look at price of goods in town markets. I figure price fluctuates much more in Floris if you have the High/Medium setting for economics. I don't know about regional productions though, which for Native, is basically the same for all areas.
PoP: Spam either Tanning or the one with the fancy Dyeworks for investments...
Troop Variety: Well, I personally think PoP wins out. As for Floris, it can probably be assumed that you will get different games between Expanded and Reworked troop trees.
Floris - Expanded Troops: Personally, I think this is pretty much a mess and seems unbalanced from my vantage point, cavalry is kingly. The high tier faction troops seem much less unique. Like the Swadians and Sarrinads both having top tier heavy cavalry, even the Khergits/Vaegir have comparable heavy cavalry. Sarrinads also share top tier horse archers with the Khergits... At the least, when it comes to top tier foot troops of the Rhoduks and Nords, they are still unique. (I think the Khergits got shafted.)
There are 7 tiers of troops, so it takes AI Lords some time to build back up a competent force, if they don't just go out and get beaten again, which can lend to AI kingdom avalanches. Lords beaten lose all troops and then have to gather troops and slowly train them back up. Lord that won the battle keeps high tier troops and gains more high tier too. (Swadians and Khergits down to 1 city, Nords overrun the world.)
Floris - Reworked Troops: I like this much more, faction troop trees are much more simple, but the highest tier is 6. Only faction troops can be tier 6, while mercs are up to tier 5. Plus, the high tier troops are much more specialized/unique to each faction. For example: Sarrinad's one top tier is now heavy infantry instead of heavy cavalry+horse archer.
PoP - Troops - Variety is the spice of life... there are so many different factions and sub-factions, each with their own sets of troops. Even the bandits have been beefed up with their own upgrade trees. Each kingdom faction has a separate Commoner troop tree, Noble troop tree and a Knight Order. Except for the fact that Cavalry is pretty much the most prevalent top tier troop type... of the Nobles and most of the Knight Orders.
Brytanwelda: Really, the only Mod I know that is not cavalry heavy... and combat is predominately toward spear/polearm and throwing. (Because I can.)
Atmosphere: PoP, the world feels much more alive... More bandits/neutrals roaming around to fight. Unique non-faction armies roaming about, similar to how native does it, but in one single large army instead of multiple groups. Quests and random stuff caused by non-factions. Sacking of towns by non-faction armies. Talking to NPCs, you can pick up rumors of stuff happening in the world. Different rumors based on relations/honor of your character.
It also helps that there is an overarching story behind the world of PoP. An established history to it. I hear it is like the 3rd 'book' or something.
Meh, wrote this up, just cause. I could probably elaborate more, but meh, you'd have to ask for something more specific.