To an extent, Joker didn't once brag about being intellectually superior.
"If you're good at something never do it for free."
"- You think you can steal from us and then walk away?
- Yeah. "
"Look what I did to this town with a few drums of gas and a couple of bullets."
Come on. The Joker didn't ever say the words "intellectual" and "superior", but everything (and I mean everything) he did exuded superiority. And seeing how he managed to pull off the most convoluted plans and still be one step ahead of everyone until the end, well, he may have been the intellectual superior indeed.
Aesthetics, and I'd hardly call the Joker's look in TDK 'elegant'.
Neither would Maroni, but let's face it, a green coat and tie and a bowler hat can't really be called "elegant" either. The point is the idea behind it, trying to do elegance but in an zany, over-the-top manner. The Joker was still wearing an expensive suit and an overcoat. More to the point,
aesthetics do a great deal of conveying what a character is about, let's not downplay its relevance here, shall we?
Complicated clues? Every 'clue' Joker left was as obvious as the nose on his face. Riddler works with puzzles, conundrums, genuine brain testers, the Joker did nothing of the sort in TDK. The Joker delt with absolutes in the film, the boat scene, the hospital, him getting arrested, there was nothing to 'solve'.
Suuure....
JOKER CARD: "
Will the real Batman please stand up?"
RAMÍREZ: Lieutenant! That Joker card pinned to the body, forensics found 3 sets of DNA.
GORDON: Any matches?
RAMÍREZ: All three. The DNA belongs to judge Surrillo, Harvey Dent and Commissioner Loeb.
GORDON: The Joker's telling us who's he's targeting.
Quite obvious, uh?
Add to that the Richard Harvey/Patrick Dent murder and the fake front page obituary. Yeah, those clues may be direct threats (which, considering other stuff he did, like saying he was going to blow up a hospital or two ferries at midnight, are not direct at all) all the Riddler can do is improve on that, make it more mentally challenging... but it's not radically different as you suggest, they're not worlds apart. They're still two psychos leaving indirect clues about where they plan to strike next, in order to taunt the police and even see if they can stop them.
So the Riddler should use carrier pigeon in film 3 for his riddles?
Nope, but you either acknoledge those similarities, like Rodrigo90 said, or you put a spin on them and make it more specific, like the Riddler only communicating through screens and distorted voices but in a very sophisticated way, maybe with a fake avatarish image... not the snuff films and the tv phone calls, if you get my drift.
Personally, I prefer Rodrigo's option. If the Joker was in fact the first large scale, massively public terrorist, and the Riddler has to retrace some of his steps, the least you can do is slightly admit the inspiration and move on.
In the Fed idea, I would even prefer Nygma noticing this and creating a false psycho criminal that purposely follows some of the Joker M.O., to add authenticity to his con, in order to lure Batman out.
But no matter what route one takes, the audience is going to see these similarities and it's better to acknowledge them instead of pretending they're not there.
To an extent all the villains are obsessed with Batman in one way or another, that's par for the course with Batman.
Many of them are not obssesed enough to even consider letting him go just because he's such a worthy opponent. Frankly, I don't see the Penguin letting Batman go or stopping other criminals from killing him because he wants that right. Neither Two-Face, except for the favorable coin toss. Catwoman would spare him for actual, real sympathy, not because of distorted admiration. In Begins, Ra's just had a very freaky idea of justice and left Bruce to die in a fire, but to die nonetheless. Keep mentioning criminals: You get the idea.
All your points are doing is skimming the surface of both characters. One is a homicidal maniac, the other is an obsessive compulsive loser, even with the vague similarities you brought up they are still completely different people, and that's what's important.
Here to touch a very good point... The 'loser' form is a one of several variations of the character. Granted, it's a very popular one, but not the definitive. Are we 100% sure an obsessive compulsive loser can be a main villain? If not, are we willing to include the Riddler in a role that fits this lessened form? Wouldn't that be a waste of potential? Byt this point in the story, any antagonist must be enhanced and their menace levels increased all the way up to fit the final chapter of the trilogy. Not 'losers' allowed. And I say this about all the villains that are considered "secondary": The Riddler, the Penguin, Catwoman, Killer Croc... if any of them is included, it must be in their greatest and most dangerous form, no less than that. Never, ever, consider lowering the bar.
And once you do that inevitable adaptation to the Riddler, the similarities between him and the Joker become even more evident. He comes from being an "
obssesive compulsive loser" to being a maniac too. Maybe less homicidal, but a maniac anyway. We can't have a villain who threatens Gotham's citizens to... rob their bank accounts.
Besides, my comparison was hardly 'skimming the surface'. Read it again, please. You couldn't have been more wrong.