Makes sense. I can respect that.I have to admit that yes i would prefer to keep it seperated from Marvel 2099 for two reasons.
First i think that the overall 2099 setting just didn't catch on as it's own thing, but rather remains being mostly remembered as the support structure for Spiderman 2099, who was the stand out character and story of it. So any other work will always just stay in the allready slim shadow of Miguel O'Hara, at least as far as i can see it.
Not to forget that using an allready established setting just creates uncessary boundaries on what could be done, used or visualized.
Which brings me to my second reason, which is that i think a completely new stand alone setting (one where ONLY the X-men, mutants and their characters exist), would allow for a far greater degree of narrative freedom, especialy in regards to where the X-men fall into the backstory and what impact the presence of mutants had on this world and for how long.
For example, instead of having to place this world in a future from our point of view, it could actualy be a future from the point of the very first X-men adventures in 1963.
Basicly in this world, there wasn't a sliding time scale. Instead the X-men were formed in 1963 and Magneto revealed the presence of mutants to the world shortly thereafter, so we are now looking 50 years ahead in a world that underwent massive technological leaps thanks to the sudden presence of mutants (Trask's creation of the Sentinels alone would have revolutionized several fields of technology).
This would also have the advantage of allowing to use the giant library of "lesser" X-men characters (New X-men looking at you) in new or old roles instead of having to create a whole new series of untested and unproven characters and designs. Especialy since this would be the ONE scenario where the original and popular character can't easily block the younger ones from rising to promince anymore, since the entire point of this history would be that they had their adventures, they ended and everyone retired or moved on because of how the world has changed.
But this specific scenario aside. That's why i would prefer a new one over giving X-men 2099 another chance.