Familiarity with home conditions, as well as India's bowling attack largely being unsuited for bowling in Australia is one reason.
As for his record in India, it's not that hard to explain. Without checking statsguru, I'm guessing Ponting's played maybe 12, 13 Tests in India? When for 3 of those Tests you've batted worse than Chris Martin, it's not suprising that his record is so poor. Missing all of the 2004 series with the exception of the Mumbai Test doesn't help his record either. I'm not a fan of cherry picking stats to make a player look as good as possible, but if you removed those 4 Tests from his record then he'd look decent in India without being outstanding, probably averaging between 35-40 (like I said, I cbf checking this, this is just a guess). This would indicate that Ponting by and large hasn't struggled in India as much as his record suggests. However, when such a significant minority of your performances in a country have been as bad as Ponting's 4 poor Tests in India, and without the presence of an epic series to counter balance those poor Tests, his record is going to look, perhaps unfairly, poor.
See also: Ian Bell's Ashes record, and Alistair Cook's Ashes record. Cook's record prior to the just concluded series was dreadful. Now, he has a very healthy Ashes average due to one epic series.