She was a bad candidate. Period:
1. No charisma
2. Not very likeable
3. Comes off as an opportunist
4. Seen as a huge liar. For whatever reason Trump seemed to get a pass (or more of a pass) on this despite lying far more than her, and far more shamelessly. But, you know, it is what it is.
5. Seen as corrupt
6. For so many people, seemed to embody almost everything they hated about politics, a problem which was magnified in an election built around populist anger / a repudiation of business as usual.
And (drum roll please) last but not least:
7. She had 54819290056 problems/scandals/whatever! Whether or not you consider these "scandals" real or just blown out of proportion, people thought they were important and it contributed immensely to her character problems. She spent almost the entire election defending herself against one scandal after another!
You could say the same thing about Trump, except perhaps the first one.
I would however add these two things:
8. Moved too far to the left. She was basically running against Bernie Sanders, still. She need to pivot and never did.
9. This might come into the charisma aspect, but Trump seemed human, and a bit spontaneous. Flawed, but human. Clinton seemed rehearsed, at times robotic.
10. Clinton looked incompetent. Looking at her email situation, she was either lying or incompetent. She chose incompetent. Look at the state of foreign relations, she looked incompetent. Clinton was a known quantity, but in looking at her record, it frankly was not a successful one as Secretary of State. The seeds of her defeat were planted in the Arab Spring.