Also remember, don't tailor the fights to the characters strengths and/or weaknesses. Tailor the fight to what the corp, gang, mission, group the characters are going against would have. The best way I can explain this concept is with the use of 'levels'. I know ShadowRun do not have traditional 'levels' but the concept is still the same. If all the characters are level 1 and they take on level 1 bad guys (because they are level 1) and then take on level 2 bad guys when they become level 2 and then level 3 for level 3, you will run into the issue of "why raise your level?"
Make the 'level' of the scenario based on what Mr. Johnson is going to pay and let the characters figure out how/what they are going to do. For example, if the characters are all 'newly created' and a Mr. Johnson offers them 1,000,000 nuyen for a run, the characters should run from this offer. The pay is nowhere near their experience or abilities. If however, the characters all have 300+ karma and a couple of million nuyen in the bank, the 1,000,000 offer may be about right based on what the characters are capable of. There have been many times in the past (when I GM) where a Mr. Johnson does not do his/her research on the runners and just takes the advice of a fixer. Mr. Johnson needs runners who are above average, and can handle difficult situations. The characters need to look at the job and decide if they should do it.
Also (and probably most important), talk with the players (not the characters). Find out what they want. If the players want lots of combat, then the world is darker with gun/fist fights, backstabbing, and general mayhem happening all over Seattle (or what ever city you are in). If the players want more of the intrigue, sneaking, and/or infiltration, then the fights become more of the consequences of being seen.
Going back to the 'level' concept, if runner team breaks into corporation A and all the opposition are level 1's, then 4 weeks later break in again and now they are level 2's, what is the benefit of getting better (increasing through karma)? Keep corporation A as level 1's and if the characters keep going against level 1's, start giving them a bad reputation or make their costs increase so they have to earn more just to live. Allow them to go back and run against the level 1 corporation for quick nuyen if they need it, but make whoever is offering them money start asking them to run higher levels. Think of it like real life, what ever hourly rate you make now, is this what you want to make in 5 years? Assuming you can live (even uncomfortably) with what you make now, don't you want more. To get more, sometimes you have to do more (at least in the profession I am in).
Remember, NPC represent people, but PC need to represent people too. Too many times I hear PC's say something like "Well, of coarse I would not do that, I am a professional.....". What I hear being said is "I am a robot with no emotions or feelings and am perfect in every way"..