I mean, it looks a lot better aesthetically, but in terms of functionality it's a bit less so (I wish there was an actual UX professional who was into this game/lurking on the forums, would be really handy to have that kind of expert input).
The faction info definitely needs to be more prominent, you're 100% right on that (took me ages to figure out how to tell which side is which), but you *might* have overdone the sizing a bit.
I'm not confident in the movement of the value/profit/weight info to the top, because it seems that you would want this information to be near the trade buttons, to minimize eye movement between them (as at the moment of deciding to trade, this would be important info to have), and if the value/profit/weight info is at the bottom, it might be better move the faction names to the bottom too (since all that space you've cleared for the faction name would be wasted up there), though maybe it could be kept at the top if it could be integrated with the topmost section (where the actual merchant is) somehow? It could make sense to have the representative of the faction right beside the name (only tricky part is where to fit their speech).
The search bar thing is... Difficult to decide on, because if you're not using it, it's definitely better at the bottom, but if you ARE using it, you want that on the top front and center, and in all other screens shown where there is a search bar, it's also at the top, so just for the familiarity it may be better to keep there.
The scaled merchant image... Toady said he wanted to center it, and I feel that might be good enough without enlarging it. One thing I definitely would want to see though is to have a "frame" around the merchant like with the items, because just having them casually in the UI whitespace like that is a bit weird (plus it would be nice to be able to click on/hover over their icon to see useful info about them).
The buttons... They look so much neater like that, but unfortunately, thinking of the mouse travel here.... It's not great to have the UI elements spread out so far from each other; maybe it would make sense to turn the mark/unmark buttons into a single toggle-able checkbox/icon (instead of being a text button) and have it aligned with the checkboxes in the item list? Since it has pretty much a similar function to the toggle boxes on the "item group tabs" anyway, and with a tooltip and good icon it should be clear what it does.
Continuing the "golden line" between the merchants and your fort might be a good idea (to further differentiate the seize and offer buttons); when it comes to the trade button, it could split both ways and "surround" the trade button, to indicate the nature of the trade being mutual/in between the 2 screens. On that same note, the trade button could maybe stand to be enlarged a bit/emphasized compared to the other buttons.
Finally, not a criticism of your design in particular; the weight thing might make more sense/would have a clearer meaning on the merchant's side, since the weight is relevant to the merchants caravans; but then again, it's also about how much you are offering them...