(Typed this up earlier without posting and see Bolo had made some of these points already. Ah well, not gonna waste the effort I'll post anyway.)
Getting a bit ridiculous now. Unless you're Tendulkar no one is playing enough games against each team home and away to be able to conclude a significant analysis in this manner. However he consistently averaged significantly more against the weaker teams, which is a stat that does hold statistical significance.
You touch on the point that he had the ability to do anything though. He could be as good as anyone against the highest quality bowling which on the surface I understand might seem to contradict my point but it's a sign of his relative inconsistency. He had the ability to be great against the best bowling attacks but over the course of his career under-performed (relatively speaking) against them as a whole.
I agree with a lot of your second paragraph here - he had the talent to be an absolute top tier great but his output didn't quite match it. Partly that's due to him being picked for Tests very young and not getting great until later, and partly because of his own decision to opt out of Tests when he was in his prime and at his most consistently brilliant.
But still you're reaching to knock him for scoring more against weaker teams. Firstly, to repeat myself, that's what you'd expect. Most players will score above their career average vs weaker teams and below vs stronger teams. That's a given. You'd need to show that it was disproportionately true of de Villiers for it to be a criticism.
Secondly, you say his biggest challenges were Aus, England and India. As a SENA batsman I think playing away in Asia was one of his biggest challenges (you made the point to Bolo above that his home stats vs Sri Lanka are not as meaningful as his away stats against them. I agree and it goes for India in that period too).
De Villiers vs Aus - great average, slightly above his career average.
De Villiers away in Asia (with or without Bangladesh included) - incredible average, above his career average.
De Villiers vs England - averages low 40s. Below career average (but not terrible).
Doesn't seem like someone who struggles disproportionately with the tougher challenges, and especially so when you add back in the evidence of all those amazing innings we know he played against quality bowling.