A lot of people don’t like the intro to fallout 3 because it gives you your backstory as a 19 year old vault dweller, however I believe fallout 3s intro is great for an RPG. The backstory may be set for your character but the purpose of fallout 3s intro is more so to introduce character development and personality. Specifically on ways that your character deals with specific situations like bullying, what you do when you see your friends getting bullied and how your character treats his friends and family. Now yes, new Vegas does allow you to have more freedom with backstory however I find character development a more important mechanic to showcase in an RPG as it’s more focused on what your character does and showing what type of person he grows up to be. It makes more sense for an Rpg to showcase character development as the first mechanic the game introduces.
My problem with the intro is that it sets too much. You're always James' shy kid that is only friends with Amata and is liked by teacher, Gomez, Stanley, Old Lady Palmer and Jonas. You're always bullied by Butch and other Tunnel Sneks, you're disliked by Overseer for being friends with Amata.
You can't do anything to change your relation with any of these characters (you can save Butch's mum, but even if you bash her head in with security batton you took from dead guard he'll always join you as a companion if vault is opened in Trouble on the Homefront).
If your character's backstory is set in stones as much as Lone Wanderer's why not give it as many moving parts as possible?
You could alienate James and Jonas to score points with Overseer, so when James escapes he sends you after him. There are so many wasted opportunities in this intro.
Now to quests you mention:
I really like You gotta shoot 'em in the head and Tenpenny Tower, so it's a shame that they're exceptions from the rule.
What's so morally grey about it? Your only choices are
What should be done with a Family?
A)Make an alliance between them and Arefu (everyone gains)
B)Leave them be (no one gains or loses)
C)Kill 'em all (everyone loses, in unpatched games Arefu becomes hostile)
Should Ian return to Arefu?
A)Yes (Ian returns to Arefu, nothing happens)
B)No (Ian stays with Family, nothing happens)
What should you do with Harold?
A)Kill him (Harold dies happy, Oasis propably dies)
B)Stop his growth (Sapling Yew convinces Harold that life is gud so he lives happily, Oasis still exists, Wasteland doesn't get plants)
C)Accelerate his growth (Sapling Yew convinces Harold that life is gud, Oasis still exists, Wasteland goes green, old guy that wanted you to stop Harold's growth is grumpy for one voiceline)
D)Burn Harold alive (Harold dies in agony, everyone goes hostile, you get nothing but some loot from corpses and lots of evil karma)
Should I kill two people with mental problems or use power of logical arguments so they both give up before someone is hurt?
A)Kill, kill (two sets of unique armour)
B)Convince, convince (two sets of unique armour)
There could be an argument about previous ones, but what is morally grey about rescuing 3 children from slavery before they're sold as sex slaves/cheap labour?
fo3 only consists of black and white decision making
Whole MQ is black and white decision making. First side quest is blow up a town (you get less money for it than for collecting colas) or not. It's the hardest game to complete on neutral karma, when you have to constantly deliver scrap and water for free and pay off preachers in breaks between selling slaves to achieve karmic balance, so I get why some people get this impression.
They mostly are, but they're exceptions from it. To only mention characters like Pinkerton or Zimmer that can't be killed until you complete
side quests that are tied to them.
I end it by saying that FO3 is a really flawed game, but I enjoy it for the most part.