I agree. I finally played Brotherhood again today after taking a week or 2 break from it, and I've experienced a number of things mentioned on the list.
Jumping and Camera
This seems to happen a lot, Ezio jumping off in a slightly different angle, missing the ledge, also the camera randomly swapping direction just as you were pressing jump, resulting in Ezio jumping in the opposite direction. Especially noticable with the romulus ruins which have a stupid timer on, where you jump to what you think is a ledge, and it either isn't a ledge, or ezio jumps off in a different direction. Meaning you have to restart because you need to be perfect for those timers pretty much, and you have to go through the annoyance of climbing up again. It's also noticable in those VT chase missions, where you have to run quickly through the hoops in a certain time frame to get gold. I also fell due to it in another one of the ruins which didn't have a timer, but required you to not lose any health, screwing the 100% sync again.
Timers
In some cases the time seems to be about right, but then with other ones it seems to be a bit stupid. Like I mentioned above, the ruins ones, there's no chance of doing it on your first time, you need to know where to go and not fall down, or else you won't do it in time. Usually I don't have a problem with timers, but they went too far with some of the times.
Instafail Missions
100% agreed. This has happened tonnes to me today, where I'd kill a guard who hadn't seen me, and he somehow detects me, it's screwed up 100% sync things, and it's even more frustrating having to constantly watch the loading screen over and over.
War machines
This somewhat connects with the above, where it kept restarting if a guard somehow detected you when he was dead, the first two war machine missions were only annoying due to that really. The flying machine and tank on the other hand, oh dear. I'm not even going to bother 100% syncing those two. The controls for the flying machine were just down right awful, not to mention you'd shoot directly at the cart, or the building, and for some reason it didn't register the hit. The tank wasn't quite as annoying to control, but I could see getting 100% sync being annoying.
I'm also going to add a few others.
Targeting
Autotargeting has always been an iffy thing in gaming, and probably will never be perfect. Sometimes it won't auto target the guard infront so you can send your assassins, resulting in you getting detected before you can. Also you'd be standing in front of an assassination target and for some reason the autotarget thinks you want to assassinate the guy next to the target, and so the assassinate move kills him instead of the target resulting in either a game fail, or the 100% sync fail.
Hiding in Crowds
Sometimes I would run into a crowd, thinking I could hide in there, and the game doesn't put me into blend mode, despite being in the crowd, causing you to have to shuffle round before it registers. Also you would randomly get knocked out of blend if the crowd decides to go straight into someone in the middle of the path and the person then knocking you out of the blend. Also some crowds wouldn't even blend at all despite there being enough people. over all it was just extremely tedious when you're trying to stay undetected.
