The thing is, pilot training may have been the issue in the Lion Air incident but that doesn't mean it was Lion Air's responsibility. Arguably Boeing sold these new planes as not requiring specific re-training (a major advantage which made their product more attractive) so it's not like every pilot is suddenly being re-trained on them until it's confirmed this is the problem. When/If Boeing admits pilots need specific training for these new systems then they will be in deep shit.
EDIT: A side note from reading the r/aviation thread, half of those posts seem to be Boeing "fanboys" being defensive of them and Airbus "fanboys" trying to lay blame on Boeing without knowing what the hell happened. It seems we always have to convert to a binary world, it's Ronaldo vs Messi, Boeing vs Airbus, for Trump or against him. People really need to take sides on everything.