The problem is Jokic isn't a traditional big. When we think about traditional bigs we think about dominance in the paint, being physical and bullying smaller opponents, that's not Jokic's game and certainly Embiid is better at that.
Jokic's playmaking abilities won't be rated as highly as they should because he is a center and that won't be the focus when people are trying to rate him. He certainly influences more on the court compared to Embiid, but being 7 foot everyone, especially ex-players, expects him to play in the paint and bully opponents, as supposed to staying out and playmaking like he does.
Embiid would've won last season as well had he not gotten injured, it would be very difficult for Jokic to win the MVP with everyone fit and healthy because he will never have the narrative in his favour. He can get as many rebounds and assists as he can, if he scores less than Embiid, the vote will go to Embiid.