I still think the Thanos snap and decimation of mutants because of it as the best and smoothest transition,and this could directly lead into HoX.Start the movie like Messiah Complex and reiterate that Destiny prophecied a great destruction of people and mutants,explain that humanity was restored by Avengers travelling in time but Loki taking the tesseract out of that universe meant mutant numbers were not restored.The Xavier mansion and school exists, but Beast is researching what happened ,why mutants who disappeared did not return.Actually the idea of HoX need not immediately jump to Krakoa ,but have Beast seek help of Sinister who is already dabbling in mutant resurrections(we can tie his efforts to secret funding by Hellfire club headed by Selene to take it into the Necrosha storyline in the continuity).Meanwhile have Cable steal the Tessaract from Loki and escape with Hope into present day and present universe to set off factions fighting over Hope just like in Messiah complex