Really, they never did reveal where homeboy got his soldierly skills from, or his weapons and tactics training.
I think that's part of what makes Half-Life interesting - the way they dealt with that. They made Gordon simply a tool. He's nothing more.
Which is also something Laidlaw mentions in that quote. You just sit there taking orders, never questioning. You're a drone that's considered a hero. HL2 makes it somewhat known that your orders may be questionable, but Gordon just goes with it.
Some people hate that, others adore it.
As for Alyx, yeah she's got her faults, but I think she fits in to HL well enough. She was a bit of a necessary evil in order to add humanity - something that wasn't necessary in 1998 but was in 2004. I'd like it more if they develop her, though. In HL2 she's like a little girl meeting her childhood hero - and having a puppydog crush.
I'd like to see her respond to Gordon being a drone. Her to start noticing he isn't the massive hero, he's just a killing machine. People point him in the right direction and he goes on a rampage.
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