1) Does anyone know what is happening to the Channel Islands in SR5? I have seen reports of France and England, but I think the islands are too small for anyone to have written about.
For the most part you're right, most islands haven't gotten any mention. The Isle of Man did have some sort of astral event, but then UK's military locked it down and nobody has access to it and nobody's sure what happened. I believe the mention was in 4E Sixth World Atlas. Like the writers, look at your setting's history and folklore background. It's not quite
Stargate SG1, but it will help you figure out which guidelines you want to border your campaign with.
2) Does anyone have any tips for fleshing out missions? At the moment I literally have one paragraph of what the goal is, how they'll accomplish the goal and what happens if they don't.
I like having more than that in related/parallel events and things that I hope the players will run into, but players are very good at taking a direction you did not expect (unless you want to be boring and put them "on rails", preventing them from having any real decision-making power). I have a vague idea of what I want to happen and improvise between 50-75% of what happens in any single game session. Any events that they sidestep I put in a text file and modify so I can tweak it later and use it in the future.
3) Is having an overall story a good idea or not? I'm used to playing towards a final boss battle with the Big Bad Evil Guy, but I know that Shadowrun isn't like that.
Instead of going towards a single final Big Bad Dragon, I would recommend that you come up with a story theme - an international terrorist plot to release Soviet-engineered smallpox throughout the world for a mundane meatspace plot. Maybe it's a new cyber-research project that accidentally created a powerful but cunning new AI that's bent on overthrowing the current world system for a Matrix plot. Maybe an insect shaman cult is plotting to re-open a gate to allow in legions of legion invaders for a magic/Spirit plot. Or you can have a street-level campaign where you never leave the city district. It depends on the scale you want, but once you have a thematic idea you can start to find ways to tie it into every character so everybody has something to do.
I'm a writer, so I love creating new plots and this is what I do as I create entirely original missions. If all of this seems too much for you, then I would look for "Food Fight" for an easy beginning that's already written, packaged, and published by the developers, and many more pre-written adventures are out there for you (I would not recommend running the Dawn of the Artifacts for a while because things can easily Go Wrong unless your characters are well-prepared).
