I think Red Skull takes this one. They're both evil as Hell itself, but Joker is more of an "insane" kind of evil, while Red Skull left the insanity part in the capable hands of Hitler and just became a megolomaniac. But as far as a battle between the two, Red Skull is far superior both intellectually, physically, and his plans are usually on a much grander "world domination" scale. Joker just wants Gotham. Red Skull wins.
They're both pretty bat-sh*t crazy.
But Joker's plans are of killing Batman and/or destroying Gotham in different ways, while Red Skull's plans reach global domination. In my opinion, it takes a bit more brains, strategy and cunning to be a global threat than it does to harass Batman and threaten any single city; be it Gotham or the occasional Metropolis.
Not to say Joker couldn't aspire to and possibly attain greater heights, but in that respect, a Red Skull he will never be.
the biggest reason i can see for people picking rs is that he is a global threat and joker is more of a local threat who singles people out and goes after them. and thats one of the reasons i pick joker. if this was who could take over the world first id pick rs. but his normal tactics of using fear, intimidation, or civilian casualities would have no effect on joker. when hes fighting cap and is losing he can grab a hostage or start a timer that cap has to stop to save a town or something and cap chooses the lesser of 2 evils joker would kill the hostages himself take rs as hostage to barter for some nazi weapons, kill rs keep the weapons and blow some shit up