This is a good read. Like I mentioned in my own post, I really hate the pre-made content for this game. I never use things like the action clock, instead favoring other pressures. The campaign I am running now is filled with paranoia and my players are constantly expressing fear they are being followed or otherwise set up, especially at times when, from my point of view, nothing is really happening. I feel like this is a much better way to create tension in the game than some artificial counter.

The GM has to prepare 5 Mission-Directives, which dictate, at which point the players gain XP.
An example: "When you deliver the prototype, mark XP."
This by nature is very rigid, and actively opposes playing to find out.
What if the players don't want to deliver to prototype? They're not getting paid, yeah … But they're not getting XP, either!

I was concerned about something similar, so I devised my own system for Karma reward. Just because you didn't complete the job successfully does not mean you didn't learn anything from it. Having run and played this game for a few years now, I find that combat focused games get tedious fast, so it's better to encourage roleplay. With that in mind, I put a mark next to each player's name (in my GM journal) every time a player interacts with another in a scene. I may add an additional stroke for exceptional roleplay or particularly inventive problem solving. At the end of the mission (successful or not), I average them together to get base Karma. Once I have the average, I then use a few modifiers like subtracting for failed mission, or adding for particularly difficult encounters.

This system works really well for situations like our current one, where we needed to take a break from SR for a few weeks. It's better to settle Karma during the break and start fresh than try to remember where everything was at several weeks later.

This implied a: How? (Bad mistake planning this!)

This is a classic rookie GM mistake. I'll share my notes as part of my series on Shadowrun, but you'll see that I tend to make bullets about information I want the players to get from an investigation scenario.

It doesn't matter to me how they get there and I often find that they will give me ideas about where to take the story next. Keeping it more open really helps take some pressure off of me. I don't have to try to lead them here or there. I can just parcel out information as it feels appropriate for the task. I may allow rolls for grilling certain characters, but often an NPC they are talking to will just give them information that's pertinent to at least get them to the next plot point, because it advances the overall story.

A classic trap less experienced GMs fall into is being too rigid with the ruleset. If you give yourself permission to make adjustments, you'll probably end up a lot happier. The game is designed in many ways to be "take it or leave it". If you embrace that spirit, your frustration level will likely drop substantially.

The most important thing of all is to have fun. If your players are having fun and you're having fun, then you are running a good game. If you are not having fun, switch it up to make it more fun. If the rules are in the way of that, change them. It's your game.