If a player has put a lot of character resources into being very good at something, let them be very good at it. If he wants to be insanely good at hand to hand combat, thats fine. And give him chances to use it. If thats what makes his character cool for him give him the chance to enjoy it.
The thing to do as well is to make sure there are plenty of issues that can not be solves by punching someone in the head. Ranged opponents, magical opponents, trolls that roll 22 dice to resist melee damage, etc. Also, put in social and technical challenges where punching the guy makes things worse instead of better. Runners need to figure out, and figure out fast, that no matter how good they are at something someone out there is better (Prime Runners) or that opposition can just bring so many more guys to the party is doesn't matter. You can be Bruce Lee's ghost with Wired Reflexs 14 and a dozen guys with machine guns is still a dozen guys with machine guns. If you build the adventures right playing smart and playing as a team will be more important than any one character. If a runner, or a whole runner team, uses violence as a first response rather than a last option then then escalating violence will be the inevitable result, and the opposition will usually have more resources in the long run. Being a successful runner is often about getting away without giving the target to much of a reason to hunt you down and take it personal. If you leave pile of corpses everywhere you go, they start to take it personal.
