You make some excellent points. I love Shazam, so admittedly I will bend my better judgement as necessary to facilitate his return even though story wise it makes little sense. I'm currently operating on the logic that the dude has forty siblings, any one of them could be written into the new "Shazam" with minimal effort.
As for the other deaths, similar "mk style" logic could be facilitated, I mean in MKX Jax literally just wakes up and walks out of hell and starts a family. That's canon. An ex-dead man retired, unretired and and is now smoking cigars and cracking wise with ninjas. That fucking happened.
As for INJ, Dick Grayson Nightwing is in the game even though he is dead (and almost entirely unmentioned in story mode, for that matter), No shortage of archery flavored family or friends of Oliver Queen could take the mantle, canary would be tough but if Fate is coming (And he is) it would not be tough for him to re-recruit the displaced Arrow and Canary for help in the obviously unexpected Injustice 2 conflict. Its not like retiring to a happy family has ever kept a super hero out of the game, Batman can't do it, Superman can't do it, Wolverine can't do it. Marvel unretired Hawkeye like 15 minutes later, just so they could run the ant-man on an arrow gag in a movie.
Lex's suit could be worn by mercy (She's already referenced), or they could write some nonsensical lex clone plot. They have options. Joker would be tough, but if there's anyone in the DCU a writer will bend the fucking rules for its the joker. Dude doesn't even have a backstory because they were tired of retconning it. That's legendarily shit writing, but we're all on board now.
I just want someone who powerbombs people into lightning bolts. It's all I've ever wanted from a dc fighting game. Well, that and the question but i'll take what I can get.
