Arcade endings are not canon.
The ending leading into the next MK will be the MKX's story ending.
This but a lot of the Arcade endings don't actually contradict the story endings, they could actually co exist. I doubt NRS has actually spelt out the story of MK11 for his through the endings but from memory Raiden/Kotal (Raiden Kahn), Kitana, Kung Lao/Kung Jin (saving Lao) and Liu Kang (king of hell) all seem to form a general arc.
And then you have other endings which make sense for world building/canonical/keeping characters around purposes like Jax/Sonya (Jax getting assassinated by Erron thus taking him out of the next few games and giving Jacqui something to do), Scorpion (make him Raiden's lieutenant when Raiden goes Kahn), Mileena (shit ending but they won't get rid of MK's most popular female character), Kenshi/Takeda (Red Dragon vengeance gives them something to do and lets them work in and redeem Daegon), Cassie (tie up Shujinko), Kano (to further the descendants theme in the future), Ermac (Shang absolutely HAS to come back) and Ferra/Torr (possibly the least likely new character to return and explains how their species works) all could be worked into the future story or could even be considered semi-canon pending disproval (namely Cassie's). To illustrate, I'll basically consider something canon if it explains something and isn't explicitly ruled out. Like when Kano and Erron talk about Erron killing Kobra: thats canon to me because it explains where Kobra is in the new timeline. A lot of the above is logical progression and I wouldn't be surprised to see them used either as plot points or 'passive canon'.
The ones that have no chance of being canon or influencing future story are Shinnok, D'Vorah and Quan Chi (for obvious reasons), Erron (because they aren't going to kill off all four of the kids and having Jax take the hit gives his arc an end and lets Jacqui breathe as a character), Cage (because it directly contradicts canon in three different ways, which is kinda impressive) and Reptile (duh). I've started to come up with a rough view of where NRS
could go and how to work in MKDA and MKD (considering MKX is a retelling of MK4) but it's purely speculative.
I kinda half expect IGAU2 in 2017, MK V IGAU/MKVDC2 in 2020 and then MK11 to be a full hard reboot in 2023. Hope not though, I desperately want this series to move away from its roster/story comfort zone like its done for the gameplay