That's a good point about the fact that flat footed does more than just remove dex bonus. That being said I'd say that the rules for acrobatics are not reiterating what is happening but are in fact applying two separate yet similar statuses to the characters.
This also explains the change in the way sneak attack works for unchained rogue.
In other words the rogue on the ledge would not have been flat footed, but he would have still lost his dex bonus. He could still have made AOOs if the opportunity arose.
As to the rest, yes I've had a few issues over the course of a year with mainly two individuals. I have no issues with my group correcting me, and have reversed a ruling many times. On several occasions this has ruined what I had thought was a very clever ploy/challenge/puzzle, but that's just learning. And even in the few events where play breaks down over an argument, if I don't change my mind and enforce things as I see them, I've always managed to salvage the day with humor. On multiple occasions I've had people in the group laughing so hard they either A) almost peed themselves or b) nearly passed out. Its a work in progress.
I also have been very generous to the pcs. They are geared way better than they should be, even though most of the things they've killed didn't have gold. Just recently I had them work through the abandoned maze of a copper dragon loaded with humorous tricks and illusions (like fake tunnels and hidden passages). There was even a vendor named Apu in the dungeon who traded them for wooden weapons that were cursed with returning. Basically while they can do whatever they want to them the weapons randomly the weapon will just show up in there hand. They also made off with one of the tricks. It was a sign that said (in draconic) Do not pull the lever, and a convenient lever to pull. Of course they pulled it (there is a gnome in the group), and the illusions of whatever they feared most came out of the wall in front of them. Instead of having a laugh and moving on one of them pulled the sign down, made a makeshift lever out of a pole and pulled it. Now I hadn't thought about it like that but when they did this I thought it was hilarious, so now they have a sign that turns any lever they put it next to into an illusion prank. I can't wait to see what shinaniganry ensues from this. Anyway, the dragon had a vision about their quest and if they passed the test (which they did surprisingly) he left them 120k gold. I also like to give xp and even stat points for solving riddles and puzzles, or even just doing something really clever.
Lastly a word on realism. Realism with magic is the key part here. Obviously in the real world no one is able to mutter a few words, use some random materials, and wave their hands as if losing their balance and create a ball of plasma wherever they want. And no, I have never disallowed a caster from casting spells because it isn't realistic. People seem to think I'm going crazy with this, but I'm not. Its not unrealistic to think a person could pick up a car in this world where strength can get that high. It is unrealistic to say they could pick up a car by its door handle.
Irregardless I greatly appreciate all of your comments. You guys/girls have helped me figure quite a few things out, and I like most of your general advice about how to handle being a dungeon master. Kudos.