Synapse is a sore spot for me because of a couple of things.
First is Length. Its not super long but there are a few missions that just don't need to be there; they are padding. They could be removed and it wouldn't impact the "Story" a single bit. It's a running joke to me whenever I am on one that the fastest man in Paragon City has us running around clicking call boxes to patrol. He could knock that shit out in like 3 seconds. Lazy Phalanxer. Chop one of the two boss takedowns (Bertha or Long Tom, you pick. While it has been said that Yin is the sweet spot for length, Synapse shouldn't be shortened to that degree. Also the mission before the Babbage Spawn mission, chop that. Do the Clockwork Baron with the Babbage at the end cause the King is bitter you took out one of his favored royalty.
Second, Clockwork King is a relatively easy AV to take out, anti-climatic considering how much harder a fight Babbage was. He needs to be strengthened to be more of a challenge. He needs to summon swarms of his mechanical menaces to attempt to overwhelm the team with drains and mez (like scores of Tesla Knights and such).
Third, just call the rescue the workers what it is, a defeat all in all but words.
I don't dread Synapse. I don't like it, I definitely don't embrace it. I do it when I have a toon that hasn't done it (very few of those left) or when a speed runner is doing it when its WST. Synapse doesn't need to be overhauled like they did Positron, just cleaned up; streamlined a little.