To make your question short, and to see if I understood it correctly, we're talking about a player who made his character a certain one and roleplays it entirely different. You added that you think that it comes from inexperience, and that he created this character after you said "no" to some "freak-character"-ideas. You want to help him roleplay the character he created.

As I see it, this problem is made from two smaller ones. The first is that he doesn't see his character as interesting because the character "is normal and normal is boring". The second is that you wanna help him understand why the way he plays the character does not fit the story-world of your game.

Helping him understand that "normal is not boring

This is the more important problem, as it stands in the basis of the entire problem. If he'll see that normal characters can be interesting his "anti-persona" will perish and he'll roleplay a normal character and not a freak one. The main trick here is to show him that normal characters are not entirely normal, i.e. "no person is like the others". In order for that to work, we need to give the character depth.

The easiest way to give depth to a character is through internal conflicts. Having goals and all is nice, but without something that blocks oneself from achieving them it is far less interesting. First thing to do is to go over his character's background and see if he implemented there an internal conflict for his character. If so, show it to him and talk with him about it. If no, sit with him and help him to come with one. The internal conflict doesn't have to be extravagant, but it needs to be there. An example one might be that he loves Vincent's sister but secretly hates Vincent himself, or another like Loves the sister but thinks that he's not good enough for there. I'll take the second one as an example for this section.

The conflict gives us a few things, a few added benefits. It gives the character 2 conflicting goals: "Get the sister and prove that I'm worthy". Now, with those two we also get a kind of an achieving-plan: "If I'll show her that I'm worthy, by getting something amazing done, she'll want me and I'll be able to get her". More than that, the character gets the knowledge that each advancement in order to achieve one goal will drive the other one to the far end.

But the first conflict is even more interesting. The character here has the knowledge that he needs the brother in order to save his lover, but he just can't stand being near the brother. He'll drive the mission onward for two reasons but he'll have doubts about his lover- if he'll marry her he'll be stuck with this brother of hers.

To make long story short, simple conflicts can show the player that even normal characters are interesting and unique. When combined with goals they force the character to take certain steps along the roads, to commit certain actions along the way, that he won't want to do but will make him doubt himself and question himself and see that his problem are far more interesting than those of every freak that he'll encounter.

Another nice way to help him see the importance of conflict is through showing him and analyzing with him certain protagonists that are normal people, from the stories and movies and series (of any form)that he likes. He'll see quite quickly that the conflicts make them interesting.

But he may say that it is not enough. For that there are a few more literary tools that might help him see why normal people are interesting. The first one is having flaws (internal or external) and the second one is using "The Ghost".

Flawed characters are characters that just like normal people aren't perfect. Those flaws can be internal (self-doubts, for example, or a mild paranoia) or they can be external (they're look frightens ordinary people, for once, or a missing hand for the other). The idea is that the character has to deal with the flaw, and one day to find the strength to overcome it. The fight for the overcoming act makes the character far more interesting. A nice example of that can be seen in The Rain Man, where he learns at the end that he can count on strangers/"dumb" persons like he's brother. Another nice example can be seen in the story of The Ugly Duckling who although looking terrible learned to acknowledge himself and to accept the way he looks, to accept his difference.

"The Ghost" is an event from the past that just like a ghost haunts the character to this day. Again, trying to cope with it is what builds a deep character. One example for this can be seen in the movie Inception, where we literally have a ghost- Cob's wife. Another example for this can be seen in the movie Casablanca, where he has to deal with his broken relationship with Ilsa. This Ghost is far more interesting as the originator of the Ghost actually comes back to his life. In Frozen we see another kind of a Ghost- the act that one feels guilty about. Elsa actually killed her sister.

All of these techniques are there for one reason- to make regular people interesting, to give depth to the characters, to make them human beings with goals and drives and psychology.

Helping him see that his character doesn't fit the world

After he understands that he doesn't have to be a freak in order to be interesting, he will be far more understandable about playing a character that fits the world. Then, try to explain to him as calmly as you can what it is in the way he played his character that doesn’t fit the world.

Explain to him that the characters are in a world where being a freak is bad, where achieving one's goals is the ideal. Each and every one for himself, as the saying goes. Give him examples from the way he played his character and analyze with him, in a one-on-one conversation where his way of acting came from. Use the background he created to illustrate to him where your problem comes from.

Then ask him what problems he has with his character, and together try to find a solution. Maybe let him be just a little bit freakish. Maybe he needs to just create a different character. This is basically between you and him. After that show the updated character to the group and get their approval.

When combining those two, you'll get a player who his far more willing to both play the character while also seeing the problems with the way he played his character before.

Combining the two solutions

When combining the two solutions you get a better player, who understands for the future also how to create regular characters that are not freaks yet far more interesting than those freaks will ever be able to be. Furthermore, you get a player who is willing to play his character as written while still making the character fit into the world. Hope any of these helped you.

Involve the players

What strikes me as I read both of these situations is that the players seem only tenuously involved in the events that occur. The major action seems to be on your side of the screen, or in the hands of the dice.

In any game, this will tend to make players dissatisfied, because there seems to be little reason for the players to actually be there. This is why combat is usually very exciting: game systems bake in a formula that ensures everyone at the table is involved during the scene. The good news is that you can make some simple changes to your style that will put your players in a more active position.

Add opportunities for the player characters to shape events

A lot of the examples you presented were of the general form:

GM: The world is in [state]. [Consequence] happens.

Players: We address [consequence].

Setting the scene this way keeps the players only reactive to the game's events. You want your players to be proactive shapers of the game world. So give them those opportunities.

Worked example

GM: "The girl feels sick, she vomits your bridge."

Captain: "Ok, we get to clean it."

This example doesn't give the players the opportunity to address the situation in any more interesting manner. By the time they get to make a choice, there's already vomit all over their control panels. Instead, you should present opportunities to the players:

GM: As you start to take-off, you can see the girl stumbling back and forth between the control stations. [Pilot], this kind of reminds you of how the new guys always looked after their first session in flight school.

You can now pause just a second here to give the players the opportunity to comfort the girl. Maybe the medic gives her a sedative, maybe the party's friendly face sits down with her and talks about something. If they don't do anything to help the girl, then sure, let her vomit on the bridge and they'll clean it up. But they had the opportunity to avoid it.

Don't rush to summarize social exchanges

In the dinner party, you seem to quickly move past all of the opportunities for character interaction. Instead of immediately telling the players what happens, leave it up to them.

At the beginning of the dinner, tell each of the players which other guests they would recognize. Ask each of them to play an exchange with somebody at the party; it could be one of the people they know, or some arbitrary person who would be there.

Let the players discover leads organically, and maybe they'll miss some of them, but they'll have more connection to the ones they find. If there is a lead that you absolutely have to give to the players (and there shouldn't be more than one, or you'll have the same problem we're trying to solve here), have that lead rudely interrupt another conversation. If something is important to you, it should be important to somebody in game as well.