I would say the skins you allow depend on the number and nature of the players. For instance, I really have problems getting the Ghost going in ANY game, and I'd be loath to have a chosen in a one-shot.
Prep-wise, all I have are a list of names for when i draw a blank, and I do prep the same way I'd do it starting a campaign. Creating classmates and such are a great way to make players invest in NPC's.
Make it as feral as you absolutely can. have NPC's killed off left and right, make the worst happen.

So we had our first run of Uncharted Worlds last night (combined with a very nice barbeque). We didn't get to see the characters in play as we spent our available 3½ hours creating them and building our little slice of the galaxy.
We began by jotting down a few base rules for how our universe would work.
1: There are fixed jump points in a network. Some of them lead nowhere but you can still get back. Jump points are stationary and rather far from the star. It takes at least several days to get there.
2: You can't fly FTL, and there's no FTL communications. However, there are comm-sattelites that constantly jump back and forth at their designated jump-points, delivering messages.
3: No aliens. At least, not yet.
4: Earth is a myth, lost in the mists of time.
5: Most worlds are shaped by the original Terran cultures that colonized them, although there is, of course, overlap.
6: There are both single and multi-system governments, with some large empires of 10+ systems.
7: Only shuttles land on planets. Starships dock at orbiting stations connected to planets via space elevator.

Here's what we discovered:
Character creation takes a damn long time compared to other AW hacks due to having to read through and select two carreers and an origin. On top of that you have to set some standards/rules for the universe to get everyone on the same page. You also have to get some somewhat detailed starting factions together. It's fun, but time-consuming.

What we hacked together:
We stole a page from Monsterhearts to create the crew. We'd decided early on that actually <i>having</i> a crew was necessary for the gameplay, as that would give me (the GM) some ready cannon-fodder/possible hostages/interpersonal crisis/story hooks. We needed names, and we needed to make them matter, their deaths mean something, other than "We lost redshirts 2, 7 and 15. Hire some new ones next time we dock". We divided them by department and then created interdepartmental relationships. We'll be doing a relationship map to keep better track.
We also drew the ship, deciding what it would look like and where the various departments were located. 
Mostly for flavour, but also to decide what crew to get sucked into space during battle. I know this isn't covered by the rules, but it really helps immersion.

What I <i>wish</i> we'd hacked:
It takes a bit to create a backstory, so what we decided we needed was a Monster of the Week-style backstory generator. It could be located on the origin sheet and would speed things up, not to mention making it easier to remember the basic backstory between characters. On top of that, it's very easy to build upon.
A faction background generator would be nice as well, as would a ship relationship (how'd you get on the vessel).

In two weeks, the trade/salvage ship HMMS Pandora, an old but servicable tub of a ship will take to the stars with its crew of miscreants, wash-outs and grizzled veterans.

Here's our design document and world creation:

World
Jump points as FTL. Fixed points link a network of systems.
Old Earth is lost in the mists of time. Considered a legend.
Humans only (for now)
Both single and multi-system governments with a few systems of 10+ worlds
Large ships cannot land on planets.

Characters:
Gregorius and (forgot name, sorry)
G is an aristocrat, third son, joined the Royal Gaian Navy and was discharged for doing the right thing against orders. High-brow, rich (well, not ready cash, his family has all the money but will help if asked. And they pay his butlers salary).
Unnamed was previous owner of the Pandora but got himself into money trouble and decided to take on an invester, Gregorious. Techhead and greasemonkey who sleeps on a cot in engineering.

Worlds: Gaian Kingdom, Greek culture dominant, monarchy, 2-system Kingdom, primary system is Gaia, Athens (capitol planet) Delphi, Sparta, secondary system is located in a galactic cul-de-sac, Elysium, penal/farming/mining colony. Population consists of prisoners and volunteers who work there (managing the prisoners) for good pay on 10-year contracts. Planet is very rich in resources but is too hot and muggy for humans to feel comfortable.

Free Trade Station Ticonderoga, expanded over the years with a hodge-podge of debris (and looks it). Governed by the guilds, very Wild-west, only trouble with the law is breaking a contract or endangering the station. The system itself has dead planets and a gas giant.

Kazue: Multi-system empire, originally populated with Chinese and Japanese, very populated. Will trade with foreigners, but is very isolationist. Caste-based society, with merchants as the lowest as they are considered polluted by their contacts with foreigners.

Ashanti Empire: Bio science, very evolved, genetic engineering, may be the next step of evolution.

The Singularity: High-tech society, cybernetics



Ship (HMMS Pandora)
Crew Quarters
VR-Suite
Shuttle bay
Stealthy Shuttle

Crew
Weapons


Bridge
Pilot: Robert “Bob” Mills. Boring, happy to work away from his wife and kids, never takes initiative
Co-pilot: Tad Andrews, disgustingly good looking flunked the academy, horn-dog
Astrogator: “Icarus”, too clever for her own good, daredevil, former lt, was only allowed to fly support ships in the navy.
Engineering
Chief: James Ellison (Jimmy)Too young but with an innate knack for machines.
Engineer: Hermann Schwartz, old, by the book, drunkard when on shore leave.
Apprentice: Petra Ellison, young and wide-eyed, 15, adorable and seems naive (a facade)
Service and Maintenance
Cook: Kostas, great cook, former private, stickler for hygiene since he gave his entire company fod poisoning
Cabin boy: Hannah Loré, Tall and skinny, wild hair, 18 years old, first time in space, naive.
Janitor: Hank Aldrin, grizzled veteran, prosthetic arm, knows everything about everybody jovial gossip, the ships “mommy”
Butler Konstantinos, Lethal, immaculate and a master of etiquette.
Cargo
Deck Chief: Jesse Williams, old and authorative, tough but fair, doesn’t tolerate nonsense, no-ones mother.
Accountant: Aleksandra, well-educated but inexperienced, tries to ingratiate herself to the family. Good eye for a good deal
Hauler 1: Sean Williams, Jesse’s son, born spacer. In a relationship with Aleksandra that she believes will end when her contract does.
Hauler 2
Medical
Doctor/Security/Armourer: Mario Velasquez, former Seargent saved by Gregorious

I know it's very late to offer corrections, but you mention Olivia Dunham from Fringe, but you spell the last name Denholm.

I'd recommend a very brief demonstration of the rules (you roll 2d6 and add or subtract your bonus) and spend a lot more time talking about the genre. Mention scenes from movies to illustrate what direction yo want the game to go. It's much more beneficial than talking about the rules. Show, don't tell.

If both are PC's, it's true, you can't manipulate. You can, however, offer strings, xp or, you know, roleplay it out. If I've decided my character hates your character, then no mechanics would make them friends. Or rather, if mechanics suddenly decided how my character felt towards someone (emotionally, not physically), then it would no longer be my character. And while I know someone will likely make a comparison with "Turn someone on", let me state that inflicting lust is like inflicting pain. You may hit me, and it will hurt, but I get to decide how I feel about it.

Personally I don't feel the need to make this a move. When you create the NPC's, which is mainly the players' jobs, they're free to create a friend. It worked just fine in the games I've run so far.
If you really need rules, you can always just Manipulate an NPC, since you've already decided you're friends, that kowledge will reflect in the demands made.

I really don't see the problem, to be honest. If all your players are homophobic, they won't roll to turn on someone of the same sex because they feel their character is straight, so they won't think to use the move.