A director putting his own stamp on stuff doesn't make it wrong.
Even in comics, different writers and artists put their own stamp on the characters and their looks, and change some stuff around to suit their strenghts.
Not making Vanessa a mutant or toning down the design for Ajax is a deliberate stylistic choice. Doesn't make it wrong. The team probably pondered for months on how to tackle some issues, and went for what's best for the movie.
The important thing is staying true to the core and the heart of the characters. And they totally delivered with the first movie. It is a faithful movie, in the sense that it perfectly captures what we all loved about the Deadpool comics and put it on the big screen.
Anything else is just nitpicking. I really can't imagine any Deadpool fan having problems with the movie they've made.