I have always seen Gibby take his time and go to the umps. Hell because he took his time and was so slow Maddon protested the game. He has certainly made the "gut" calls and that was mostly either due to the 1st base coach's opinion (Ryan Goins beating out the tag a few games ago and the 1st base coach stated he was likely in), challenging at home plate when players are stated to be out but aren't (Melky in Okaland on the phantom tag and Melky again when he was blocked at home vs CWS).
Those "gut" reasons are usually due to the players having a feeling that the call is wrong. There is no issue with him making those calls as most managers would.
Wagner's arm injury could have resulted regardless if Gibby put him out longer than he should have. I will agree that Gibby certainly needs to be better in managing them (bring Loup in situations he shouldn't, letting Casey/Santos pitch in games he probably shouldn't have gone to them and the occasional McGowan f*** up) but overall he can't keep on using the same guys over and over each game. This is certainly a area that I agree needs assessment but not for the reason you are stating.
This I disagree with. He usually platoons quite well. When a certain pitcher is announced to the game he knows to switch out certain players for others given their splits. This has arguably been one of Gibby's better strengths this season. It just sucks that the players he has on the left are high power strike out guys (I.e. Rasmus, Franny) and his depth of righty hitters that can hit lefties recently improved as it was mostly Tholleson before.
Again, I'd argue that even if you swapped Gibbons with any other manager in the league, this team would still have such a record. He wasn't the reason players kept on making errors last season and as much as the media loves to throw the term "fundamental baseball" that is something players should already know how to do from the minors up.
I agree on this as well. Gibby is going to be the scapegoat as undeserved as that is. For everything you listed I could list against AA (terrible trades: Jomes for Rogers, Happ trade, Dickey trade), raising payroll for 2 consecutive years and potentially 3 and likely missing the post season all 3 of those years, unable to find a starting 2nd baseman, holding too long to assets to lose them for free (should have traded Jansen last year), etc.