Right, I've a bit of free time on my hands atm and both Dark Light and someone else who's contacted me over PM seem a bit lost on the whole 2099 deal so I thought I'd crap out a little bit of a primer to go with our GMs intro.
Marvel 2099 is an extremely 90s cyberpunk what-if alternate future. Think rampant megacorporations that rule vast swathes of the world and the corruption that ensues, scientific and technological advances that are often detrimental rather than favorable for mankind and the planet, massive social inequality, human modification and loss of identity and a hectic underground world of mercenaries, freedom fighters, hackers and the like. Now filter that through 90s comic books where two of the original lineup stars were The Punisher and Doctor Doom. There's some serious themes but this isn't exactly the most serious and thoughtful medium.
As for the links to the regular Marvel universe. The line was thought up as happening a bit over 100 years into the future when it was published in 93, with the story being that the "Age of Heroes" of Earth 616 came to an abrupt end due to an unspecified catastrophe that set civilization back. Prior to the point where the comics start, there were no active superheroes in 2099, and the superheroes of old have become myths and legends with worship of Thor and Hulk playing part in stories. Links to the old heroes are oftentimes tenuous at best, so the whole "son of" deal wasn't exactly prevalent.
By way of examples, Hulk 2099's backstory involves the Knights of Banner, a group experimenting with Gamma Rays to try to recreate the original Hulk. Punisher 2099 is a member of the private police force who suffers personal tragedy and is inspired to take up the mantle after coming across Frank Castle's war journal. Much of the plot of Doom 2099 involves a great deal of doubt over the identity of this Doctor Doom and whether he is or not the actual Victor. One of the major crossover plotlines was an attempt to create a false pantheon of Norse gods in order to quell the new wave of heroes. There's plenty of room to be at least slightly more creative than just a future descendant of X or Y.
In short, 90s cyberpunk Marvel with an emphasis on the "punk" where the heroes of old are often taken as myths and legends. Near future technological dystopia with some actually serious themes but the focus is more on flashy laserguns, crazy powers, flying vehicles, neon lights and a good deal of violence as the way to go about dealing with The Man.