I started answering this question and realized that my ideas raged totally out of control. My apologies for how ridiculously long this answer got, but I hope somebody finds it useful.
When I'm doing the initial campaign planning, I pretend I'm designing a TV series. I also make sure that I've got everybody's character concept in hand before I start plotting out the episodes(adventures). Once I've got that, I also know exactly how long the campaign will last. That's because I plan two episodes for each character, but I also design each episode to be played through in a single game session.
From there, I steal the basic design concept from Babylon 5 and Buffy. Every episode has an "A" plot, and then a "B" subplot. Each character gets 1 A Plot, and 1 B Plot. The remaining A/B plots go towards the BBEG. (Big Bad Evil Genius) The hardest part at this point is deciding what the BBEG's master plan is going to be. It has to be something that can develop over the course of the season (campaign). Early episodes have subtle hints at the BBEG's plans, but usually by 1/2 way through the season, the characters have realized that something bigger's gonig on.
Usually, I sketch this out in Excel, with 4 columns. I use the first one for the episode number, the next for the A Plots, and the 3rd for the B plots. Each character's name/concept goes in one slot. The first episode always focuses on a character (always either the team leader, or "The New Guy" if somebody joined an existing group). The last episode focuses on the BBEG. I then make sure that people don't have their A & B plots in consecutive weeks.
Then, I take the fourth column and throw in a very brief episode concept. For instance, if I'm doing the rigger's focus episode, I might put in "Car Chase." For a mage, I might pencil in "Toxic Shaman." For Episodes that focus on the BBEG, I use the fourth column to briefly summarize what he's done for that scenario. (Aquires crucial spell component. Buys out Minor corp. Brings in Vampire Bodyguards, etc.)
My last step in Excel is to fill in the B Plot in the 5th column. This will usually be something minor that happens in the background during the course of an adventure. A street sam might get a call from a contact that his new gun has come in. There might be an incidental contact with one of the BBEG's lieutenant's who's doing something peripheral to the scenario. If the B plot is for the BBEG, it has to be something minor. Especially in the early runs. Usually, I don't want my players to realize the BBEG has done something until two or three episodes later here.
Then I write out the "TV Guide" synopsis of each episode. This is probably the most important part of the early stages. I try to keep these fairly brief. Basically, I just take a paragraph to flesh out the core ideas of my initial plots, and give two or three sentences about the key NPCs that I'm going to introduce.
Once I've got all of the season synopses done, it's just a matter of doing detailed sketches of all the NPCs for the season. If an NPC isn't going to show up until episode 5 or six, I tend to let them percolate for a bit, rather than rushing and trying to cram everybody in before the season has started.
Finally, I wait until the week before I'm running an adventure to actually write it out in detail. That way, I can take into account what's happened in "last week's" episode in the details of the new episode. When I get down to doing this, I open up Word and cut and paste the relevant line from Excel in, and then follow it with the Episode synopsis.
Then, I go to town. Since our weekly game sessions last about 4 hours, I write in three critical scenes. For a Shadowrun, especially the early season episodes, these are usually just "The Meet", "Legwork", and "The Run." Sometimes I'll need a fourth "Cleanup" scene, but not always. Episodes heavy on investigation might have two or three Legwork style scenes. Episodes heavy on combat might have two or three "The Run" scenes. If I'm starting out "in media res," I'll just have one long "The Run" scene, then throw in a "The Meet" scene part way through as a flash back to explain hwo the mess started.
For each scene, I write down the key NPCs/critters and any information that I think will be relevant. I don't stat out everything. If it's not a combat encounter, I only throw in the relevant skills. If things get out of control, I wing the other stats.

That's forced me to get good at winging things. I also add in any rules that I think I'm likely to need a reminder of, or a page reference if I think it's likely to be needed. Finally, I note the key goals for the scene. IE, what info the NPC will impart, what gear they'll hand to the players, what conditions'll cause the critters to break and run, etc. My scene write-ups tend to end up at around 1/2 a page each. Often for the key scene of an episode it'll go to a full page.
I usually don't bother with maps at this stage. I keep a dry-erase Chessex mapboard on the gaming table. When things get to a combat or "dungeon crawl" level, I'll sketch things out, but most of the time I just describe the situation to the players before that.
The other thing I do at this stage is generate player hand outs. I write up any news clippings they might get, print out maps if they're likely to find them, and find a photograph for key NPCs. (Usually with a visit to IMDB. This week, the part of "Harlequin" is played by Johnny Depp.

)
As I run an episode, I write down any NPCs that I had to introduce spontaneously, and any groups that I referred to so that I can re-use them in the future. I keep another Excel spreadsheet full of recurring characters.
Usually the early episodes of a season start out with the players getting to learn each other's strong and week points. During this time they're also first meeting the recurring NPCs. As you mentioned, it's important that I've got the recurring locations set up at the start, so that they're consistent throughout the campaign. Later episodes are when they really come together as a team. While I've got a lot less overhead for designing background material during the later episodes, I've got a lot more work setting up the dramatic impact.
The last arc I plotted out (I've just finished episode 2) details a chess-like game between two great dragons. (Ala the Harlequin/Ehran battle in the original Harlequin adventure.) It's a 12 episode arc, and I went with an Elemental themes to the Focus episodes. So, in each of the 5 BBEG build up episodes, the GD that the PCs work for is seeking to show dominance over the opposing GD in one of the 5 elements. (Earth/Air/Fire/Water/Aether) The concluding episode will feature the cataclysmic fight between the dragons. For every scenario that the players succeeded in winning an element, "their" GD will have an edge over the opponent. For every episode that they failed, the reverse will be true.
Gah, that raged out of control.

Hope somebody actually reads it.