1. THE MOST IMPORTANT ONE: Ninten & Ana love each other! This isn't even a theory! It's a Fact! And not only that, but, this also means that Ninten & Ana is the only completely canon couple in the Mother series, main character-wise. At the end of Earthbound Zero Ana recieves a letter from Ninten impling that they are still a couple.
2. Ness' mom has blond hair and blue eyes. So does Ana. On her clay model, Ness' mom carries a frying pan. (and a spatula.) Ana wields a frying pan in EarthBound Zero. Co-inky dink anyone? probably not. Also Ness' mom's true identity can be anyone, it's not like her name is mentioned in the game!
3. Ness' shocking physical appearance similarities to that of Ninten. Ness has to get those looks from somewhere because most noteworthy is that, he certainly did not get that black hair from his mom! The gene for black hair is dominant. That means that for the child to have black hair, at least one of the parents must have black hair, and his mom is blond. Another thing is this. Ness' dad never appears in the game. In fact, EarthBound's credits pictures Ness' dad as the PHONE. And for your information (HIS DAD'S NOT A PHONE. DUH). So since Ness' dad is never shown in the game and Ness looks alot like Ninten, that gives you room to think that Ness' Dad would possibly be the black haired Ninten.
4. As I said before, to have black hair, at least one of the parents needs black hair because it is dominant over blond. Tracy has blond hair. To have blond hair, both parents must give you a gene for blond hair, or the hair will turn out dark. Ninten has black hair. But remember this, his mom is blond. That means his father of course has black hair too. Since Tracy has blond hair, she got genes to be blond from both parents. Ninten has a blond gene from his mom, and Ana has it from both parents. Thus, Tracy's blond hair and Ness's black hair.
5. Where'd Ness get PSI from? Ninten proves that you can inherit PSI. The game states that he inherited PSI from George, his great grandfather. If both parents have the same trait and because both Ninten & Ana have PSI, then that makes it very possible for Ness to get it from them! Although, maybe Tracy doesn't have PSI on the first glance, but who knows. Tracy might be like Lucas. She may need it to be awakened.
Well. You got those things down. Let's correct the time issue here.
Itoi made the game take place in 1988 in the original Mother. He later realized that he wants fans to speculate what year it's in so in Mother 1+2 and EarthBound Zero, he put "80 years have passed since then" instead. In Mother's prologue, it says "in the early 1900s." That means it takes place from 1900 to 1904. (because you know when rounding tens...5 and up goes to the next ten.) If you go with 1900, 80 years later would be 1980. So keep 1980 in mind. Ninten and Ana are 12 in 1980, according to Mother.
EarthBound takes place in 199X. Again, Itoi wanted fans to guess what year it was. That X can mean many things. It can mean any digit between 0-9, OR the roman numeral. X in roman numerals is 10. Nineteen Ninety ten? That's 2000. (Mind you, people thought the world would end in 2000 back then, so it actually makes perfect sense that EarthBound takes place in 2000. Another thing, EarthBound actually does take place in 2000, the librarian in Onett tells you "Return the Town Map in 2001." Hmm...) Ness is 13 in EarthBound, and 2000-13=1987. Ninten and Ana would both be 18-19 by then. Now keep this in mind, pregnancy lasts 9 months, and that's almost a year. So chances are, they were 18 when they had *insert 3 lettered word here*. Picture it this way: Ninten and Ana get married and move to Onett during the pregnancy because remember in EarthBound, Ness was born in Onett? And Remember in EarthBound, Ness' father gives Ness his cap? Well, who else other than Ninten has that red and blue baseball cap like that in the first place? (Ninten switches to his blue cap after he gives Ness his red cap) ONE MORE THING. If you notice in the flashback in EarthBound after defeating Carbon/Diamond Dog and acquiring the final melody, the house has hardly any furniture in it. What do you think that means? They obviously moved there. (This information also indirecty proves that Lloyd is Dr. Andonuts, Dr. Andonuts is Jeff's father, Lloyd and Jeff are nerds, Lloyd and Dr. Andonuts both hide in trash cans, and they both have white hair)
With this information, Ninten being Ness' father makes perfect sense.
Ninten is obviously older than Ness so in SSB4 he should be at least 14 years old.