1) How about " A woman doesn't fall for a mute, she becomes good friends with him due to his previous actions and surviving traumatic situations with him"? I've covered this already in that it's implied and only just. You're reading into something that's not actually there and even if it was, it's a valid storytelling technique in video games to use a silent protagonist (as is the wheel in Mass Effect). Your imagination is supposed to fill in the blanks in these situations. All the Call of Duty campaigns use the silent protagonist to good effect and there are many games that utilise it. You not liking it is completely subjective.

I'm beginning to suspect you're secretly infatuated by Alyx to the point where you think she loves you/Gordon (even though she's barely flirted with Freeman) which has lead you to conclude you're actually a nerd and have to compensate by trashing a storytelling technique used by the game. VG Psychology!

2) You've reworded the question from a qualitative "How can you enjoy HL2's story when its so thin and just A>B>C?" to a semi-quantitative "How can HL2 have such a vast story when 70% of the game is devoid of story?" using some arbitary calculations based on an abstract of the game. It's essentially the same question reworded slightly differently so look back over my previous answers.

We didn't talk much at the first meeting but it doesn't really matter how it happened. I was in my late teens, she was in her early 20s. The attraction wasn't purely physical (although that plays a significant part). I suspect certain mannerisms are sub-consciously noted/familiar and you're just drawn to that person because of it.

Of course it takes time to get to know someone (it's possible she could have turned out to be a psycho , good thing she isn't!), but certain people are just drawn to each other for whatever subtle or sub-conscious reason.

Good friends with a mute after 10 minutes...Doesn't sound much better. 
Well if the conversation is implied, then where does filling in gaps end? If it's not there, it's not there. Arbitrarily filling in the blanks is pointless. Using your "imagination" is just an excuse rather then a legitimate reason - for any plothole or case of bad acting I could use my imagination to fill in the blanks/iron out the issues. In CoD you are a soldier so it makes a lot of sense that you don't speak. Plus the CoD stories are hardly praised, in fact MW2 was a complete joke. If I wanted to use my imagination, I'd go and day dream. 

You are nevertheless praising a game for it's story even though the vast majority of the game has nothing to do with any sort of deep storyline. That puts HL2's story on par with most FPS' stories. Praise the storytelling mechanism as much as you want, but again, that's like having a Ferrari with an empty tank. 

10 minutes? The friendship develops throughout the entire game. I'm pretty sure if someone (even a mute) is pivotal in rescuing your father that you'll treat them as a friend. 

Anyway, whether you like it or not, it's legitimate storytelling technique. Older RPGs and older story heavy games in general relied heavily on a players imagination for the simple fact the technology wasn't available at the time. In fact, games like Planescape Torment and Baldurs Gate are often praised for their story but had little to no animations and relied on the player to fill in the technological gaps. Whilst HL2 doesn't have those limits, the use of player imagination to fill in gaps is only because everything is shown directly to the player in First-Person. Everything is directed to you so your imagination/character is placed directly into the Gordon Freeman avatar. It's kinda like reading a book written in first person.

Most of the game you aren't anywhere near Alyx...
Now you are just skirting the issue that filling in the blanks isn't a legitmate excuse for characters acting as if the silent protagnist has spoken. Imagination is good for books, but not for a post-2000 FPS. You weren't filling in gaps left on purpose, you were making do with what the tech provided. Having Gordon silent was a choice made by the devs rather then something that couldn't be helped. 

If I wanted to use my imagination I'd read a book. Plus with that reasoning you could argue that every game is a masterpeice by just using your imagination to conjure up the necessary scenarios required to make the game brilliant. 

Now on the contrary I'd argue that SotC does a much better job with a silent protagonist partially due to the simplicity of the story, which makes it all that more believable. One guy and his horse, out to save a girl/woman for a mysterious reason. Due to the lack of others in the world, it makes sense why you are silent, plus it also fits the vast beautiful scenery very well. 

Yes it's on purpose and a design decision. Gordon Freeman is an avatar of yourself, so your imagination is simply to fill in his personality with your own. It's not a big leap in logic considering it's always kept in first person perspective. You aren't conjuring up scenarios.

As for SotC, I'm not entirely sure Wanda counts as silent. He has one companion in the game and he calls his name relatively frequently. Considering the relationship of trust between Wanda and Agro, I actually think that's fairly important in the grand scheme of the game... even if it is only one name/word, the relevance is huge.

Bzzt. Wrong answer. You are not meant to fill Gordon with your own personality, otherwise you would have much more freedom. If you were a narcissistic power greedy lunatic you wouldn't be helping them would you? And Alyx wouldn't take a liking to you either...

Freeman isn't an avatar for yourself in the way that Commander Shepard is. It's meant to be seen that you are Freeman, a scientist saviour out to help the good folk on earth. 

He also whistles for Agro...I can't see how you can fill in the gaps for non-existant conversation but say that calling for a horse somehow breaks the silent protaginist idea? If you are imaging conversation then Gordon's anything but silent...

Lol, there's no such thing in this context. Just different methodologies and techniques to acheive immersion and storytelling. If you can't relate to the characters in front of you (in HL2) in any way, then perhaps you are a narcissistic, power greedy lunatic?

And the point of a silent protagonist is to allow you to place your own ideas about how they sound, their personality and even imagine part of the conversation. The fact that Wanda says anything at all breaks that because you now have a point of reference for his voice. It works in Shadow of the Colossus because it actually reiterates his loneliness and the fact that Agro is the only one he has to rely on.

Er what? If Gordon is an avatar for you then why does the game force you to do everything? Unload a mag into any resistance fighter and nothing happens...

Imagine part of the conversation?! No, that would be bordering schizophrenia. Either the conversation is there, or it isn't.  Making conversations up is no better then pretending the storyline, graphics or gameplay is better then it is. "Oh the movement isn't clunky, it's obvious that the main character just hurt his foot...". "The voice acting isn't bad, they just are stoned". 

You press a button to make him say something. That really doesn't break immersion as you are making him directly say something rather then say something you wouldn't. If you pressed X and he said "YO AGRO WHERE THE FUCK YOU GONE MAAAAAN?", yeah that would immersion breaking. But he doesn't.

I was praising SotC. Calling for Agro manages to serve 2 puposes: Actually getting your horse and reiterating that your only companion in the vast desolate wasteland is your incredibly loyal stead. It's just a different method to convey emotion in the story and one that works well in SotC's implementation. I don't know if it was done on purpose, or just a fortunate side effect, but it works either way.

Anyway, let it go mate, it's obvious you just can't appreciate HL2's particular storytelling techniques, but a great deal of others do.