Well, were the Deadpools supposed to be connected to the xfilms story line? I don't think they were. I think Deadpools 1&2 did exactly what they were supposed to: establish Deadpool exists in the same universe, have a few xmen cameos, but in the end, it was Deadpool's film and story.
That's pretty much what I'm saying. Though to go one step further the first movie also actively wanted to keep Deadpool at arm's distance from X-Men. Remember, Deadpool came out a few months before X-Men: Apocalypse. At the time, the X-Men franchise was on solid ground with Bryan Singer back at the helm and Days of Future Past being a big hit that left people generally happy and passed the baton to the McAvoy crew.
This made tying the X-Men to the R-rated Deadpool risky. Did they really want the X-Men associated with a violent movie filled with cursing, nudity, and pegging? So they let him play around in the universe, but only a little, and not with any characters that have been established within the X-Men franchise. Even the one character put on loan isn't the same one that we remember. All arm's length just in case this smallish-budget experiment blows up in their face.
Skip forward a couple years, and we have the opposite. Apocalypse disappointed pretty much everyone and left the X-Men franchise in disarray. Meanwhile, Deadpool got a ton of love, hype, and cultural credit and is now Fox's biggest active IP. Tying Deadpool more closely to the X-Men franchise now makes a lot more financial sense, doesn't it? Plans are made to put him on a legit X-Men team and the X-Men play a much bigger role in his movie. Fox wants people to think of Deadpool when they think of X-Men.
Tank mentioned Fox's accounting department considering Deadpool a part of the X-Men franchise. Perhaps. There marketing department surely wants the connection. But if Deadpool had failed or had been hated and Apocalypse had been awesome, Deadpool would have been quietly orphaned.