But the Avengers movie was based on both 616 and Ultimate versions.
But not in a fixed or equal ratio. The makers of the Ant-Man
movie are not going to be somehow compelled to use a certain percentage of Ultimate stuff whether it's a good idea or not. Naturally, like the creators of any adaptation, they have the freedom to reinvent the character however they choose, drawing on whatever elements of past portrayals they like and disregarding the rest. Nobody's holding a gun to their heads and saying "You have to include 50% Ultimate content."
The Ultimate creators' choice to latch onto a single mistake (on both the character's and creators' part) in Hank Pym's life that got blown hugely out of proportion in fandom and base their entire characterization on it served their purposes, their goal to create something extremely dark and edgy and... well, whatever the hell Millar and Hitch were trying to do. But comics today tend to have a fairly limited readership so they're more prone to be targeted at a particular niche. Naturally a tentpole motion picture is going to be created with a much broader audience in mind, and naturally if Ant-Man is the sole hero of the film rather than a supporting character as he was in the Ultimate comics, they'd want to portray him sympathetically. So they'd have zero reason to make the same creative choice that Millar and Hitch made with the character. More likely they'd base their version of the character on the more appealing aspects of the 616 version, and ignore that one unfortunate, accidental moment with Jan.