In my opinion, they should have a challenge system. Each team should get 2-3 challenges per match, and if they're wrong then they lose one. And you can challenge absolutely anything, but the play has to reach a natural conclusion before the challenge takes place.
That way, no-one could ever complain ever again about an incident going against them, because if you didn't challenge it then it's your own fault. And if you believe a legitimate goal had been scored against you, particularly early in a game, then you'd have to weigh up whether or not you challenge it, like plumb LBWs in cricket.
There is always the possibility that managers would save their challenges for goals, but if they did this then they can't ever legitimately complain about other decisions that have gone against them, because they could have challenged them. Equally, if you've got a challenge left at the end of a game then you might as well use them on anything; this happens in other sports.
It wouldn't be perfect, but it would largely, or possibly completely, prevent unfair inconsistencies, and every single goal being checked. Managers would soon stop challenging every goal when they lost a challenge, and then couldn't challenge something that went against them later in the game.
You could also show replays in the stadium, as happens in other sports, and this would negate the, I believe justified, complaints about the match-going experience being ruined. And there wouldn't be any argument about 'VAR looks at this, but not at this', you could challenge everything via replay, but you'd have to be discerning in the way that you did it.
By implementing this, everything gets looked at, if you don't get consistency with officiating then it's your own fault, any stinkers should be ruled out, and if they aren't then its the fault of the coaches, and supporters could be more involved in the whole process. It would arguably also stop dissent against officials, as if you really 100% as a player believe that foul play has occurred then you could advise your manager to challenge it.
I think this would be massively preferable to the current scenario, where every single goal gets looked at, and you never know if it's going to count or not, but then other stuff isn't even considered, and VAR regulates over certain scenarios far, far more than others.