A couple of things caught me off guard during my very first corporate contract negotiation which I had full control of, less than a year out of college. After day 1 of our multi-day negotiation, my counterpart had just started pumping milk towards the end as she was a new mother, followed by the owner introducing me to all the extended family within the organization I'd never met before, and capped off by physically walking me through to meet the employees that he had personally hired from his church groups. It's not the act itself, but it was the fact that I was dealing with a family operated business, real people, and we had just finished a very heated discussion on how I (my company) was going to be decreasing their sales in the coming years (causing job losses within their organization). I was on their home turf in their facility, and even though the whole company was pretty open and very friendly with me like friends, I'd still say this was a bit unexpected & was caught off guard. The whole situation just tugged on me emotionally, as I was trying to negotiate the equivalence of pennies for a multi-billion dollar entity, whereas the millions for this small family owned business means so much more to their team, their families, their community, etc. That was a tough one emotionally for sure, especially at that age for me, and even more so because they all treated me like I was a part of their family organization. Also, my apathy for the profits of the corporate entity I was representing also swayed me quite a bit as I had no true vested interest and I would much rather a small business have more leverage in the deal.
As for preparation, this is the most critical step for me. I want to know everything! I prepare to know as much as I can not only about the deal, but the folks across the table I'm in discussions with, their entity overall, their community, their overall goals and desires, etc. Literally anything and everything I can learn. I try to gather as much as I can throughout the process from the other party, which can definitely compile on if it is a long negotiation (sometimes spanning years). If I have a partner, or team, then it is even more important to get everybody on the same page and understand how you will operate.
To make it real estate specific, I've prepared by speaking to neighbors, city officials, lenders in the area, like-property owners, and have even chilled at the neighborhood bar chatting with "locals". Also, seller permitting, I've developed friendly relations with the existing tenants of the buildings and try to engage in casual conversation slowly inquiring more about the asset, and they usually do end up letting some key information slip that you can use in discussion with the seller to negotiate a better deal for you. This is in addition to understanding your counterparty as much as you can.
Negotiating to me is not as simple as agreeing on a number and shaking hands, especially as you deal with larger & more complex transactions involving multiple parties. It involves significant preparation, and in many cases there will be multiple rounds of negotiating in between even more preparation.