Also, I would create "information maps" or "clue maps" for an adventure. It should outline various pieces of critical information with numbers and thresholds. Those pieces COULD be connected to specific people, but I would consider making them somewhat flexible. There is some great advice for adventure design in the
Gum Shoe system and
GURPS Mysteries. I highly recommend both for ideas designing SR adventures. Basically the research and planning leading up to the run IS a mystery. The runners are collecting Intel to create the best informed plan. You can structure your information map accordingly.
1) Give each piece of Intel several vectors to the runners. This way, if they screw up finding a piece of Intel, it simply takes more time (and perhaps Nuyen) to ferret it out. If you look at the default presumption for complex tasks and retries in SR, the penalty is usually just more time/resources. Resource management is an important aspect of the game.
2) Give each piece of Intel two links to another piece of Intel. Create a web. Again, this builds in flexibility to your "mystery" so the players can still experience your idea (and plan for the run) even if they take different paths to get there.
3) Note the numbers on the map (Nuyen, thresholds, et al). This will be a handy quick reference for the game. You can put check marks next to the ones the players discover.
4) Create 3 x 5 cards or handouts for each piece of Intel. Give them to the players when the figure something out.
What does this do for you and the BBEG?
First, you can design your BBEG in the spirit of what you imagined for your story. Even if it is a pretty decent threat to the runners, the Intel you offer should give them sufficient warning and planning opportunity. After thinking about the "Glass Cannon" problem, I don't think addressing "The Game System" is the desired approach. I think the solution is in the execution. How you plan an adventure or even the campaign is going to be paramount, even more so than the stats on the BBEG. Since there are no real "encounter balance" rules, I think this is line with what the designers felt the game will support. After all, the BBEG wasn't born in a vacuum and then engineered to be a specific "threat level" for the PCs. It (he/she) should have a natural place in your setting.
Secondly, in the spirit of "natural placement of BBEGs" you should then design your BBEG encounters with this mind. Not really tailored to any specific running team, but in line with what you think your BBEG would have regarding resources and power. SOME of this information should be available for the PCs to find.
NOW, this is not in spirit with the resources I listed above. I don't think SR was designed with "encounter balance" in mind BUT you can use the mystery planning advice above to your advantage in presenting encounters and events.
Some people will approach the design of an adventure as "realistically" as possible. The bad guy IS going to murder the clone on April 14th at 7pm and the runners either get there or they don't. This is a valid adventure idea. Racing against the clock (especially when the runners KNOW when the clock runs out) can be an awesome adrenaline surge capped by exhausting victory or crushing disappointment. What if the runners DON'T know about the clock? Then it's just blind luck followed by cheesy angst. The players WILL think you're a twinkie ass hat, even if they don't say it.
I would suggest the bulk of BBEG events and encounters to be planned in a similar manner to the "Intel Map" with some flexibility built in. What's the point of an awesome event or encounter that takes place without the runners present? How are the players going to experience your awesome? Exactly. How does this help our "Glass Cannon" problem?
First, you can plan out encounters to take place after events that set up the runners to be in a state that makes the encounter more challenging. If the runners just got ambushed by a pack of hungry ghouls and are down ammo and energy, the REAL encounter will be just that more challenging. If encounter A (infiltrate bad guy safe house 2) takes place after the Intel is gathered on the safe house then create an encounter B (bank robbery gone bad) across the street to be triggered before the runners arrive. More police on scene could cause the runners to abort or at least modify the plan. What are the stats for my bank robbery? Who cares? I just changed the whole playing field and I didn't have to crack open one book to do it.
Second, if accomplishment A triggers event C that then triggers an opportunity for the BBEG to be alerted to shenanigans, you have the "BBEG knows you're coming" scenario I spoke of in my previous post. NOW, make sure that then triggers a piece of Intel the runners can learn so they KNOW the BBEG KNOWS about them, and then the planning and ultimately the encounter becomes that more challenging.
So, you start out planning the adventure with circles on a piece of paper with your plans, events that then create circles for encounters (adventure map). Use those to create pieces of Intel for your information map. Then create little circles for triggers that generate optional pieces of Intel you note on the information map and link them back to your adventure map. Give your circles multiple ways to be triggered/found and you can remain flexible to your runners' actions. Plan ahead to make the run challenging before, during, and after combat and I think the "Glass Cannon" thing can be a feature versus a defect.
Why a feature? Because combat is deadly. NO ONE goes into it unaware or foolhardy. Bad guys aren't going to directly confront a heavily armed Shadowrunner team head on. Nor should the runners be eager to confront their targets in a like manner. Challenging encounters require more than the BBEG having the right stat distribution. Like real like, the situations presented in the game should factor in everything that real soldiers/criminals use to their advantage.
Just my (now) three dollars...