I agree that many of Bernie's problems stemmed from the fact that he was only familiar with Vermont style politics but I'm not sure that Bernie himself recognized this fact. He certainly didn't acknowledge it, even when he was advised that this was the case.
He had no experience governing in a place as diverse as NYC but that didn't stop him from running to Brooklyn in an effort to boost his NYC credentials during the primary campaign to tout Brooklyn as instrumental to shaping him as the person he became in his life.
Aside from that, Bernie just made numerous faux pas on the campaign trail and became caustic when he got cited for them.
For instance, calling black people in the South 'low information voters' certainly didn't help his case. Instead of truly acknowledging how his comments could be taken, he insisted that others just didn't understand the spirit in which he uttered those words. He never went much deeper than that though, just seemed to barrel along.
Bernie seemed unwilling to listen to the concerns of voters of color, insisting his ideology was best. He came off as a brittle, inflexible unable to adapt know-it-all.
Hillary, on the other hand, during her campaign, spent an hour at a nationally known hip hop radio station and acknowledged her past foibles, especially the super-predator comment, which she apologized for. She acknowledged how hurtful those words would come off. She also made a fair point that many black churches and community organizations, whose leaders were exasperated by the devastation of the crack crisis on their families and neighborhoods, took a tougher, less forgiving stance and she opted to fall in line with them.
(FWIW, I think those church and community leaders hoped that law enforcement would treat the crack crisis the way they now treat the opioid crisis--with a degree of humanity but soon realized that the people would be much harsher toward their communities, arresting and jailing addicts for long sentences, wreaking even greater devastation in families and communities, but that's another story for another post).
At the heart of the matter between Hillary and Obama is that fact that both are pragmatic people. The emnity stemmed from their two "camps" rather than the two of them. It was pretty well known that some key Obama campaign staff disliked Hillary but except for maybe Bill (who had his own issues), I don't think there was animosity from Hillary's key campaign staff. People forget that Hillary spent time in the Senate where she was used to quickly putting aside ego to build consensus. And I do think that Obama was genuine in wanting to build that "team of rivals" and believed that Hillary would be a great fit in his cabinet.
FWIW, even considering his remarks in their 2008 Democratic debate where Obama seemed to hesitate and then say "Oh you're likeable enough, Hillary", I honestly think that Obama really didn't think Hillary's 'likeability factor' should matter. He no doubt, recognized that people's impressions could often be skewed, some people certainly had negative feelings about his wife Michelle (remember that hideous cover of The New Yorker?) so he knew that the likeability metric was pretty superficial. I propose that that was of no consequence to him, he wanted a capable, reasonable person he could work with, even if she was tough and I suspect that he knew he'd find that in Hillary.