This is actually a lot of what we're trying to do with Season 4, actually (The new Seattle series).
For a home campaign of Missions Season 3, Manhattan, I'd suggest a few things...
1) Affiliations
Affiliations are a little screwy. They were a cool idea, but the implementation ended up a little wonky. The idea is that as you're doing adventures, you can "come to the attention of" one or more of the corporations that run Manhattan. You can affiliate with these corps, and get little side jobs to do for them. IN theory, this is cool.
But... The implementation is off. the Corps magically always know what you're doing, where you're at, and are able to contact you to give you your "side mission" no matter what, even when you're trapped in a tunnel underground with no matrix service!
Plus sometimes the side jobs can end up being very... Involved. You're supposed to keep your affiliations a secret, but that gets hard to do when suddenly you have to go off mission for something. or worse, try and do something counter-productive to the team's mission. And sometimes these little side jobs can end up being an entire adventure into themselves. Not as big of a deal when you're running this at home and have plenty of time, but when you're trying to fit the adventure into a 4 hour Convention game slot, it's very problematic.
I would suggest that you A) Make the affiliations a bit more open. Give each corp a "Contact" (Even if they simply call themselves Mr. Johnson), so that there's a direct face for the affiliation. And two, don;t worry about being so secretive. I would also consider only allowing one or two affiliations per character. It's easy by the second half of the season to pick up 6+, and some of the rewards get a bit... Crazy.
2) Definitely look over all the contacts for the season, and try and hand them out as early as possible. A couple of key contacts show up early, and reappear in several missions. But a lot end up being one shots, which is kind of sad, as they are some great contacts.
3) Play up the Neo-Anarchist vs Corp angle a bit more. It gets touched on a couple times, but due to the unfocused nature of the Manhatten missions, I don't think it was played with nearly enough. Manhattan is a corporate Enclave, strictly run and controlled by the corps, but you've got this group actively working against them. Classic Shadowrun and Cyberpunk themes right there.
Good luck!

Bull