The whole attitude towards it from the referees themselves is probably the biggest problem with VAR. It's best exemplified by an occasion where VAR worked well. I can't remember the event itself but there was some audio released a while back, in which the linesman said that he was holding the raising of the flag until play had stopped, because he believed someone was offside, but he wanted to let play continue. It led to a goal being scored and the linesman then raised his flag. VAR checked it and determined it was onside so the decision was overturned and the goal was given.
The linesman was so apologetic for the incorrect decision and the rest of the officiating team were consoling him for it. It should have been received in the exact opposite way. It was an excellent process (triggering, I know) and resulted in the right decision. The linesman should have been receiving praise for holding his flag and letting the move play out. Instead, their reactions highlighted the way that they see VAR as undermining them or making them look silly. And that's it's biggest problem. Until they look at refereeing with an understanding that they're fallible and that VAR is there to help, not undermine, there will be a tension with it that results in dreadful non-decisions.
I've been saying that for a while, but maybe not as articulate as you. I would even argue it's not just the refs that need to change their perspective. Football as a whole (media, players, managers, supporters) needs to change its attitude towards VAR. It shouldn't be seen as this higher authority deciding whether the ref has made a mistake (which going by the VAR protocol isn't the intention). It should be seen as a means to get to the right decision just like the linos are. If a lino signals for a foul the ref hasn't seen, it's not taken as the lino overruling the ref, it's seen as them supporting the ref. The same attitude should be applied to the VAR.
The problem is that not even PGMOL are using VAR that way, by basically giving the VAR the power to decide whether the ref goes to the monitor or simply makes the decision for him (like the Doku kick not being a foul). That's a fundamental mistake in the way the VAR is applied in the Premier League (and maybe in other leagues as well). It has been made clear by IFAB, that the ref is the person who makes every decision in a match and is in charge of the whole affair, but the way VAR is used at the moment, you have the ref making a decision and then the VAR making a decision (more often than not confirming what the ref has said, because apparently they don't want to make them look bad). That's how you get decisions like the Doku one or the Odegaard handball. The right way to deal with those would have been for the VAR to tell the ref that what he has said about the incident is not what has actually happened (players just coming together with the Doku kick and Odegaard not putting his hand on the floor). Then the decision should have been made by the ref, to look at it again himself. Instead, you have the ref saying it's not a penalty and then the VAR saying again it's not a penalty. It's two decisions made by two separate people, which goes against the principle of the ref being in charge of the game.
There are cases where it's fine for the VAR to make the call, because they have the means to do it (and those are "objective" decisions as mentioned in the VAR-protocol), like drawing the lines for offsides or saying whether a foul happened in the penalty area or not. They should not be making subjective decisions though like with Doku or Odegaard. The ref should be the one making that call and in both cases, he wasn't.