That Penny Arcade strip is like a zillion years old.
Let me provide you with some perspective "of the time". IIRC, I bought Shogo MAD about a week before I played Half-Life for the first time. I never finished Shogo after that.
I finished Shogo three times or more, I only ever got through Half-Life once. To me, the basic gameplay and various guns are simply much more fun in Shogo.
Your mileage may vary, but Half-Life is a difficult game to measure the importance of, because so many of the features that made it stand out from the crowd back then are just "how things are done in first person shooters these days".
Everything about it at the time was just sublime though. Present day (now past) black ops setting, unusually restrained protagonist, cleverly AI'd military soldiers (I still remember the first time one lobbed a grenade at me to flush me out of cover), and a wide variety of weapons from the beautifully mundane (crowbar) to the enjoyably ridiculous (snarks, hornetgun, laser gun thingy).
Shogo stood out to me at the time only because it was the closest thing I'd ever seen to an manga-styled game, and IIRC, it would soon be displaced by Bungie's "Oni".
Ooh, Oni. BRB, Gotta go vote for that on the list of games I'd love to see on GoG :)