I suspect the problem with the Ninth Doctor was a fairly straightforward one - he's actually in a believable line of descent, as a character, from the Doctor as played by William Hartnell, Jon Pertwee, Tom Baker, and Colin Baker. Dump in a good solid dose of post-Time-War trauma, and you have the Ninth Doctor. The Doctor always had the arrogance, and the rather blunt and cold disposition toward his companions, the sense of being something Other (something Better), the inability to suffer fools graciously (or indeed at all) and so on. It's just in the Ninth Doctor, the gloves are off, he's all out of fucks to give, and he's being Himself as hard as he can, because that's all he can be at the moment. He's not interested in passing as human any more, because he's the only Time Lord left now (as far as he knows at that point) and if he denies who and what he is, he's killing his culture and his people in a very definite way.

He was a wonderful character to re-create the series with for Old-School fans, particularly long-term Old School fans who'd seen more than one regeneration back in the day. But for New-School fans, he was confusing, abrupt, confronting, and hard to relate to.