I realize that I have no way of providing independent corroboration for most of what I'm about to tell you, so feel free to take this with a grain of salt. Regardless, this is my understanding of the larger issues behind this, derived from the opinions of people in the entertainment and licensing industries.
Background: I graduated law school this year from a school with very strong IP and entertainment law programs. One of my classmates worked for Marvel on the West Coast in licensing and media before coming to law school, one of my teachers did extensive work for Marvel in the 70s and 80s, and other classmates and teachers have worked and continued to work with Marvel licensees past and present.
The consensus is that Disney has asserted full control over Marvel's licensing, in contrast to pre-Disney and the immediate post-takeover period when Marvel was allow to largely dictate its own licensing strategy. The line of thinking is that Disney doesn't want to mess with the creative and editorial process when it comes to the comics themselves: comics revenue is a virtual drop in the bucket of Disney's bottom line, Marvel management and editorial have proven themselves capable of protecting the essential marketability of the characters (the Clooney/Nick Fury fiasco notwithstanding), and because the comics are essentially subsidized test marketing for film and television storylines.
However, Disney is not going to be nearly as hands-off when it comes to properties that reach a broader and deeper (and therefore far more profitable) market: video games, television, toys and assorted merchandising. That's all stuff that Disney sees extensive value in vertically integrating into the empire. If you think back to the early and mid-00s, Disney used to be a lot freer when it came to licensing out properties it didn't see much value in; Tron 2.0 and the related comics are the examples that first leap to mind. Current Disney management doesn't share that philosophy though, preferring to keep properties out of sight completely in the belief that this "builds demand."
So where Marvel would have licensed out a cult, limited-appeal character like Deadpool for a rate it found reasonable, Disney will say no and keep it off the market for as many years as it takes for Deadpool to be featured in a film or television show before blowing the doors off with a multi-level, carefully coordinated licensing blitz that is owned by Disney at every point, from ship to stern.
This presents a specific and real problem from a video game perspective. Normally Disney would just license Marvel characters to Disney development studios exclusively. Bad enough, right? No more Marvel vs Capcom, no more Raven X-Men/Marvel games. What makes it even worse is that Disney's efforts at cultivating AAA development studios have failed. I mean, FAILED. They've shut down Black Rock, Propaganda, and Junction Point for underperformance. Avalanche and Wideload do cash-ins and mobile games only. If they're not going to license and they can't develop, how exactly are Marvel video games going to come to market?
From what I understand, this hasn't been addressed at all. Maybe in a year or two some exec will notice that licensing revenue and royalties has dropped off and see the value in licensing again, but for right now? The future is grim.
Like I said, most of this is secondhand stuff I've pieced together from multiple people. Marvel isn't too concerned about it because they've never cared much about licensing apart from how it added black to the budget, so you won't hear complaints from that end. The licensees aren't happy at all, but what can they do? They're not going to sour relations with a monster like Disney over something like this.
Hope this helps explain some of the behind the scenes motivation.