Straight up; some characters are going to be good in combat, they're supposed to be. there is nothing wrong with that, it is the bread and butter for two character archetypes: physical adept + street sam.
Mages can also be devastating in combat.
Thing to remember is that shadowrunners are supposed to be good. they have to be good, otherwise they die. if they're only as good as corpsec, then they dont live to the point where they get good.
Shadowrunners should be able to walk through standard corpsec + ganger mooks relatively easily and a dicepool of 10 is a good starting point for characters and is usually where non-combatants like deckers/technos finish up as well
Agi 4, pistols 3 (semi-auto +2) +laser sight 1 =dicepool of 10 and that is super easy to get; a very small investment for most players.
What I would say is that if combat is taking up 1/3rd of your games as your player said, then perhaps combat is happening too frequently? if the spotlight is frequently on the street sam because you're always fighting, start doing other stuff. give the decker more chance to shine {btw, logic 6, hacking 6 (+ hosts +2), hot sim 2 =16 is not unreasonable at all if you need to break into corporate hosts!), chuck in a car chase or two for your rigger, have a wagemage turn up in the corpsec to challenge your mages or build in heavy astral security.
in otherwords, dont over emphasise one aspect of the game. if everyone gets chance to shine, this problem should go away. and yes, your payers might need to suck it up and optimise a bit more, primary skills need to be 10 or higher so account for opposed rolls and -ve modifiers and still have a chance of success.
Also, a mage shouldn't be huffing and puffing about combat dicepools, a reasonably built mage can totally outshine a well built street sam in terms of utility in a fight
btw a munchkin build is usually one where it is so incredibly good at what it does that it practically never fails, it is also absolutely terrible at everything else!
You're looking at the old pornomancer face type who had a con (seduce) dicepool of about 25+ out of chargen iirc but didnt know which end of a knife was the pointy bit