He has a natural talent for hardened mental defense by White Council Standards, which unfortunately in the case of Mental Magic is kinda like saying you are the best swimmer in the kiddy pool.
Well... I think there are two different things going on here. Harry has an extremely powerful will (and stubbornness)... that makes him hard to
change/influence. No one else in known history resisted a Fallen's coin-shadow for even a tenth of the time, much less actually changed it.
But he didn't have any useful training/skill/experience in defense against
direct mental attack as of DB, so Corpsetaker could overcome him. By GS he seems to have learned a lot more though ... it's still not one of Harry's areas of talent the way it is for Molly.
OTOH, I don't think that Harry is as bad off as all that even by DB... Corpsetaker is both incredibly experienced (she was operating before the French and Indian War according to GS, so she's in the same age class as Eb and the Merlin at the youngest) and using a rare and incredibly powerful form of magic that's hard to defend against. Sure the White Council's mental training is bad by Corpsetaker's standards, but Corpsetaker might well be the best in the world in that particular area...