Here's a rough sketch to pencil in. This advice is going to be fairly optimized given your description of your first session. It sounds like your GM isn't sugar-coating anything.
Attributes A, Magic B, Skills C, Metatype D, Resources E
With Attributes A
BOD 4, AGI 7, REA 5 (8), STR 5, CHA 3, INT 5, LOG 2 (bought with 10 karma), WIL 5, EDG 2 (bought with 10 karma), MAG 6
With Magic B
Improved Reflexes 3 (3.5) - great initiative
Combat Sense 1 (0.5) - good for dodging, but doubly good for always getting to roll surprise
Critical Strike [weapon of choice] (0.5) - to hit harder with your close combat skill of choice
Adrenaline Boost 1 (0.25) - gets those odds of 3 passes up to 99.6% and the odds of 4 passes to 33%
Attribute Boost 1 [AGI] (0.25) - on average, a couple extra dice for your attacks
(1.0PP of whatever you want)
With Skills C
Firearms skill of choice 6 (+spec)
Close Combat skill of choice 6 (+spec)
Sneaking 6 (+spec)
Perception 6 (+spec)
Influence Skill Group 2 (a fig leaf common at most tables, even if you'll never be expected to make social rolls)
Running or Gymnastics 4 (from Magic B, pick Running if you took Wall Running adept power, otherwise Gymnastics)
Now, that seems pretty concentrated, doesn't it? Well you can round things out with a whole bunch of rating 1 skills for 2 karma a pop. Leverage your strong attributes. Even just Skill 1 + Agility 7 = decent dice pool. Options include:
Locksmith
Palming
Pilot Ground Craft
any Athletics skill
Con
Intimidation
Disguise
Tracking
Computer (useful for Matrix Search)
Arcana (which you'll need to initiate)
Metatype D leaves you stuck with 1 Edge, so buy it up to 2 with 10 points of karma.
Nuyen E is obviously bare bones, so buy it up to ¥26k with 10 points of karma.
Next, Qualities.
Ambidextrous is fine but there is no mechanical benefit to having a sword in each hand. For guns, ambidextrous only helps if you want to load each one with a different ammunition type so that you have the option of tazing some fools and murdering others. A sword in one hand and a gun in another is also viable, and pretty badass, but usually not necessary.
I strongly recommend a mentor spirit. They are bargain priced, add good bonuses, have reasonable disadvantages, and add a ton of flavor. Dragonslayer or Raven are good choices. Maybe Shark if you want to punch things instead of stab them.
Catlike and Natural Athlete are good values, but you may want to prioritize karma for skills. Aptitude is a lousy value. 14 karma for one extra skill point - which, in this case, will likely bring your dice pool up from 15 to 16 - isn't worth it. That's more expensive then your first initiation will be!
Broadly speaking, I would allocate the karma like this:
+25 starting karma
+25 karma from negative qualities
-10 karma for Logic 2
-10 karma for Edge 2
-10 karma for ¥20,000
-5 karma for mentor spirit
= 15 karma for other qualities and rating 1 skills
Picking up skills will make you more rounded right away; picking up qualities is the better long-term investment because they double in price after gameplay starts. It all depends on how concentrated you want to be and what the other skillsets are among the other characters at the table.
I won't get into gear right now because that's a big bucket of inifinity. Generally speaking, prioritize higher Availability items that are harder to track down after gameplay starts, like an R4 fake SIN, or APDS ammo.
That's a starting point. I'll let other agree with me or contradict me as they see fit.