These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
That One Level: As expected, there are a few missions in which getting full synchronization can be a huge pain.
Sequence 7's mission, "Supplying the Revolution". A raft carrying vital supplies is headed down a treacherous passage in the Bayou, and runs into a massive and lengthy ambush from both sides of the waterway. Aveline has to dart between islands and take out as many soldiers (some of them elites) as possible before they completely destroy the raft. That's a difficult task in and of itself, but there are also three punishing optional objectives that make it pure hell.
First: No swimming. This often means that Aveline will have to clear a large group of soldiers before the raft moves away from her and the opposite bank, as the raft is often the only way to reach the other side without touching the water. For the same reason, this also means she can't just go on ahead and kill every enemy beforehand.
Second: The raft cannot fall below 50% health. And the raft is extremely fragile - a few shots is all it takes to bring the raft down below half. It can happen extremely quickly, given how many enemies are firing at it. You have to not just be extremely quick, but also a little lucky.
Third: Use melee weapons only. Just when you thought you could simply shoot anyone before they could threaten the raft, in comes this aggravating constraint. The whip can fortunately still be used, but it takes a lot more time to drag a musketman over and finish him off at close range than it does to simply shoot the guy - especially in a frantic mission where every second counts.
Pretty much everything in Sequence 9. The first mission requires that you hold off a stream of guards for over one minute, while in the Lady persona. (Bonus points: killing them before the minute is up will also fail the objective). The next two missions - the last in the main story - each require that Aveline take no damage whatsoever while facing off against some very tough enemies. There are timed objectives in those two missions as well: you must kill all of Agate's hallucination-enemies in under five minutes, and the final Citizen E in under two.