Vad has thrown pretty spirals ten yards over the heads of wide open receivers on a critical play, but you have wiped it out of your mind in your fanboy ecstasy. He has overthrown open receivers a couple of times as well, but worse was over throwing a covered receiver when receivers were open short. He has also blown reads on many other plays you don't notice because you don' t know what was supposed to happen.
Watch how the coach reacts. He was upset with Vad not because the play was wrong or blew up. Vad executed incorrectly. If you review old games you will see him do the same to Tevin, more last year than this year, more the previous year than that. ( And, unlike fans, he does not blame or credit the QB on every success or failure. If the fault was a missed block, or incorrect route, then that player gets the grief. )
Decisions are the issue, not ability. And only the coach is a good judge of those decisions because only the coach knows what was supposed to happen ( both running reads and passing check downs ) on the plays.
Look at the situation in San Franciso for an analogy. The backup got in and played a great game because of his stronger arm and athleticism. Because of that game he got a start. Then he arguably lost the game with mental mistakes.
The press, most former players, is split on Harbaugh's decision. Some see the upside and say play the hot hand. Others have seen the hot hand go cold suddenly too often and say go with experience every time. Either way the coach has to make the call and probably second guesses themselves every time it goes south.
I was surprised not to see Vad play more in the second half because I missed the first half entirely and saw us down by two scores. I just watched his series and he had some great runs and one good pass. Judging by CPJs reaction, he messed up badly on a key play and that seemed to end his play for the game.
Vad will play more when he minimizes his mistakes more.