Here's what I can gather:

Jennifer apparently only married Marty because she felt sorry for him.
Marty was always grumpy, because the car accident took a big toll on his life and forced him to give up his music.
Marty and Jennifer apparently couldn't afford a real wedding, because they got married at the Chapel O' Love in Las Vegas. (They couldn't afford to rent proper wedding attire either, because Marty wore a t-shirt with a tuxedo print)
Even though Marty Jr. is a wimp around Griff and his buddies, it doesn't stop him from being a smartass around his family. And unlike his grandpa, he at least tries to stand up for himself but ends up giving in to peer pressure.
It seems that Marty Jr. really wants Griff and his gang to like him, and that he almost considers them to be his buddies.
Marty Jr. apparently doesn't have a car, but if his parents can't afford a better place than Hilldale, then they definitely can't afford to buy a second car for their son.
Marty Jr. apparently never hoverboards because Griff and his friends seem surprised to see him on one (it was actually Marty Sr at 17).
Marlene really cares about her brother because she tries to bust him out of jail.
Marty and Jennifer were having marriage problems despite Marty's claims that they're like a couple of teenagers.
Marty Jr. really seems to like watching TV, and he got annoyed when his dad told him to wear his goggles at the table which plays only two shows at once, as opposed to his usual six.
Despite not being very close to his father, Marty Jr. still looks up to him.
Marty Jr either doesn't care about his appearance or he just couldn't get a part-time job to help repair the sleeve on his jacket.
Marlene seems to be the typical teenage girl, and gets very annoyed when her phone conversations are interrupted.

Before: Marty Sr was very grumpy, and he was estranged from his family.
After: Marty Sr was a loving father who has a close relationship with his kids.

Before: Jennifer is often tranked and is very distant from her family.
After: Jennifer is a loving mother who sometimes acts as the disciplinarian.

Before: Marty Jr was an insecure wimp and doesn't hoverboard.
After: Marty Jr is more confident and takes after his father's car-surfing hobby.

Before: Marty Jr has never learned how to play the guitar.
After: Marty Jr inherits his father's guitar talent and has a band.

Before: Marlene and Marty Jr are very loyal to each other.
After: That's still true.

Before: Marlene is a typical teenager who caes about being popular.
After: That's still true.

Before: Marlene likes veggies on her pizza, while Marty Jr just like plain cheese.*
After: That's still true.

* The Extended Pizza Scene shows Marty Jr picking the pepperoni off his pizza.

Marlene also seems to be very close with her Grandma Lorraine. Are they still slose in the new timeline?

Yeah, they would be - and, of course, Lorraine would proud of her son in the new timeline.

Marty Jr might be friends with Doc's sons Jules and Verne, who are now grown up and are scientists themselves. Maybe one of them could take Marty Jr on a time-trravelling journey

Oh, and he would have stuck up to Griff too, Griff could be working for the McFly's, like waxing thier car.

I think Marty will also be able to get a girlfriend in the new timeline.

You mean Marty Jr? :)

Yep. Marty Jr.

I think that was because Michael J Fox is a vegetarian in real life. I think it also showed Marty Sr helping himself to veggie pizza.

I don't know if he is now. In a recent Rachael Rae interview, he mentioned about cooking a chicken dinner - but he could've been cooking it for the rest of his family. Do you know why he was (or is) a vegetarian? Is it for health reasons?

Anyway, I don't think he was a vegetarian until 1990 - and the movie was filmed in 1989. I guess you're not supposed to read too much into the pizza scene - but I just figured Marlene to be into health food, and the rest of the future McFly family not so much. It was kind of an issue of contention in Family Feud. I see her as sort of a future fashionista - even though an early draft did have have her (as Doris) be overweight.

BTW, I'm not opposed to animal right activists - but I have to admit that I'm a little leary of them, for the same reason that I'm a little leary of Christian Evangelicals. I worry that they might look at some of my habits disapprovingly, and preach to me about why my ways are "wrong".