Shinnok coming back, Evil Raiden, they were both taken care of 10 minutes into the new game.
Dark Raiden is probably the biggest wasted plot in the entire series. We had TWO Dark Raidens in two timelines and Midway/Netherrealm managed to never do anything cool with him.
I think Dark Raiden could be awesome if we saw Dark Raiden go full militant. It's still Raiden, he's just giving zero fucks now. Have him rally Earthrealm for full war, strike ALL of Earthrrealm enemies and possible enemies. Essentially MK3 in reverse - Total War with Outworld, Netherrealm and any of the Realms that's full of assholes bent on conquest.
Remember how MKIII and the MKIII part of MK9 was all about Outworld invading Earth? Like that but reverse. Soldiers fighting magical warriors, F-35 flying over Outworld shooting dragons, Shaolin Monks and Lin-Kuei attacking the Tarkata en-masse. Earth invading Outworld.
Everyone is like "Hell yeah finally Outworld is getting its just desserts" while having the dawning realization that Raiden is growing unhinged and tyrannical and becoming more of a loose cannon (imagine Dark Raiden telling the Elder Gods to fuck off). You can even some good guy on good guy action as the good guys break into a civil war about it, leading to another version of the Liu Kang vs Raiden scene (except no one is being manipulated by Kronika here, because she's dead). Imagine Dark Raiden as an OP final boss, as Raiden finally shows his full godly power to the mortals (its implied since the very first game that Raiden is way more powerful than he lets on but Da Rules don't let him use his full power on the mortal world).
Hell, that could be a good Mortal Kombat 2. Just start in a familiar-esque timeline and go from there.
They need to reboot it again to remove any traces of multiple timelines and grand, universe-destroying characters/plots. I don't know how they keep falling into that trap.
I think the idea of the Timelines was cool, kind of "Everything is Canon" situation that could expand the universe a lot. It also built into what was made in MK9.
I think it was too early to go Multiverse/Timeline on the FIRST game of the New Universe. You don't go multiverse until your new universe is established, duh.