It's most likely that Shinji being called at the last moment was intentional from Gendo as a part of the plan. Not a wrong call.
Simply because it's part of Gendo's plan doesn't make it right. In fact, it makes it even more of a mistake.
For Bardiel battle, once again it's only Shinji who is held accountable for wrong decision. AND for endangering NERV with his tantrum. Gendo just played hard commander in harsh times. Shinji was just childish.
Gendo's "hard commander" act was idiotic and arrogant. If he had instructed Shinji to simply subdue 03 and remove the entry plug, then Shinji wouldn't have reacted the way he did, and 01, 02, and 00 could have taken on Zeruel together.
Wille was elaborated to hell and back that they were explaining things to Shinji, but he once again was childish and bailed out. Once again, no ones fault but his.
When did they explain to him that he had caused Near Third Impact, paving the way for Nerv and Seele to initiate Third Impact? All they say is that if he gets in an Eva, they'll kill him. Not exactly helpful.
The only one I could agree with you was about Kaworu making initially wrong call, because Gendo outplayed him. But once again this is pushed aside, since he tried to stop Shinji and then sacrificed himself to stop Shinji's screw up, so he more or less gets absolved.
If Gendo hadn't outplayed Seele, then Seele's Fourth Impact probably would have started instead. Kaworu's manipulation of Shinji blew up in his face (well, actually around his neck)
Kaworu's sacrifice doesn't change the fact that he screwed up.
As long as Shinji works for NERV he is a soldier that's expected to perform his duty.
A forcibly conscripted child soldier with barely any training and at least one mental disorder that would probably make him unfit to join any military force.
Who's the idiot who conscripted this guy - oh