It was never confirmed that director Tim Miller would return for Deadpool 2 after his record setting outing with the first, but it was assumed to be the case. It looks like it was supposed to happen too, but alas, he is out now.
The Wrap report that their sources say this is due to a creative clash with Ryan Reynolds, who has a lot of power over the character. It seems the two had a rocky relationship for a while, and they disagreed on what the second film in the series should focus on. They report Miller wanted a "stylized sequel", while Reynolds wanted more of "the raunchy comedy style".
It seems like the last straw might have come over casting choices, as Miller wanted to cast Kyle Chandler as Cable, which Reynolds wasn't so hot on. The studio ended up backing the star, and thus it seems the director left.
This is all alleged goings on, and one source even said the break-up was amicable, but it does seem like Reynolds really does have a firm grasp on the character. If the report is correct, he has casting and other creative controls, which is rare. However, there is no cinematic Deadpool without Reynolds, so I can see why the studio is backing him. Let's just hope this was the best thing for the production rather than just a tiff that will hurt the end product.