Daisy chose to stay with Tom for the simple reason that she never intended to leave with Gatsby. She could not leave someone who comes from a long line of wealth for a man who, despite how much money Gatsby has, is still a "poor boy*" because of how he made it.

* The phrase, "Rich girls don't marry poor boys" was mentioned in movie adaptations, but never in the novel. This quote supposedly stems from a conversation Fitzgerald had with a woman similar to Daisy.

The primary way in which Tom and Gatsby are alike is their wealth; however, they differ tremendously in everything else, particularly how they earned their money, how they treat those without as much money, and how they end up in "the end," to borrow a phrase from Nick Carraway.

Tom and Gatsby are tremendously wealthy. Gatsby has a "menagerie" while Tom could play polo on his lawn. In fact, F. Scott Fitzgerald's decision to have their homes face one another, while convenient for plot, provides a symbolic mirroring. Tom is on one side of Long Island and Gatsby on the other, "less fashionable" side. The houses facing each other is not the only device Fitzgerald uses to suggest the two mirror one another. Their relationships with Nick also provide a way for the two to be compared. Nick is Gatsby's only real friend, as evidenced by him showing up at the funeral, while, to Tom, Nick is only a companion to tow around with him as he sees his mistress. But the two, regardless of the loyalty Nick shows to Gatsby, use Nick for one reason or another.

Obviously, Tom and Gatsby are different in how they earned their money. Tom came from a wealthy family and inherited so much money that he was able to bring down polo ponies to his home; for Nick "it was hard to realize that someone in my own generation was wealthy enough to do that." Meanwhile, Gatsby grew up with nothing. He came from a mother and father who "were shiftless and unsuccessful farm people..." After almost inheriting a good sum of money from Dan Cody, Gatsby eventually gained his wealth through bootlegging.

Finally, one major difference in the two is the loyalty they show Daisy. From the beginning of the novel, it's clear that Tom is unfaithful to Daisy. Jordan Baker tells Nick in Chapter 1 that Tom has a mistress and everyone knows. Then, when recounting the story of Daisy's honeymoon, Jordan tells Nick that Tom got in a car accident with another woman. Gatsby, meanwhile, stays loyal to Daisy until the end, telling Nick, "I suppose Daisy'll call too" when it is clear that his relationship with Daisy has ended and she will remain with Tom.