Think about it. 

Man-Thing, Swamp Thing, and the Heap

Deathlok and OMAC

The Hulk vs. the Flash (their powers would not really affect each other, so both of them would have to think/act outside of the box)

Captain America and Wonder Woman (with a fight between Steves Trevor and Rogers) and throw in Uncle Sam too

Spider-Man, Blue Beetle (Ted Kord), and the Creeper

Captain Atom vs. Mar-Vell

Daredevil and Green Lantern vs. the two Scarecrows (Marvel's and DC's)

Captain America vs. Captain Nazi

Adams-era Batman vs. Sienkiewicz-era Moon Knight

The Phantom Stranger and Dr Strange

Thor & the Asgardians vs. Wonder Woman & the Greek gods

And I'd like to see how Superman would handle some of Marvel's heavy-duty villains like Dr. Doom, Ultron, Kang. the Destroyer, the Red Skull with the Cosmic Cube, the Mad Thinker, Galactus, the Enchantress, Proteus (from X-MEN), Dormammu, etc.

Batman vs. the Riddler--but in a really cool, smart, intricate storyline...something we've never really seen before!

Likewise, I think there's a great Spider-Man vs. the Chameleon story waiting to be done!

It seems that more could be done with Baron Zemo in a Captain America story.  The Red Skull and Zemo should be like Luthor and Brainiac to Superman, but you hardly ever see Zemo as a master villain except in old AVENGERS stories.

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I don't want it too much, but the keyword is "sparingly". Done every now and again, it's better. Picking up a Spider-Man issue and seeing Mandarin on the front cover would be fun (I always enjoyed Spider-Man taking on dictators like Doom, so always craved a Spider-Man/Mandarin encounter).

I just think there are so many never-before-seen (or rarely seen) encounters loaded with flavour. We've all seen the trouble Iron Man has had against Hulk - even when wearing his Hulkbuster armour. Imagine Iron Man in his 'normal' armour going up against Juggernaut or Abomination. Imagine Cap alone against the Sinister Six. And just how would Professor X handle the Leader?

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So much brain to worth with!