Bane: A mundane super soldier (genetic augmented strength, etc), or juicer (uses combat drugs and hormones) that is unusually intelligent and charismatic. A leader inside a terrorist organization, capable of going hand to hand against standard power armors and hefting heavy infantry support weapons. 

Catwoman: An agility/dexterity based physical adept (using parapsychic powers to augment physical ability) Catwoman is a themed professional elite thief. An excellent example of a freelancer shadowrunner, not evil but not good, a potential foe. Some high end electronics, an encounter suit (skin tight of course) and some light concealed weaponry, there you go. 

Clayface: Storm rifts are strange events, eruptions of cosmic energy/poison/radiation. Clayface was a normal human who caught the brunt of a surge blowing out of a rift. His flesh became pliable and viscous, moldable. With the eruption of parapsychic abilities (a not uncommon occurrence) he found with contact, he could temporarily mimic other people's appearances and mannerisms. This is a function of a mental/mind controlling parapsychic ability tied into a horrific shapeshifting curse.

Harley Quinn: Not everyone in the Cosmic Era is a mutant or parapsychic. Harley is just a demented woman who is attache to the next fellow on the list. She is a zealot, and she can range from an elite mook with good gear and skills to being a chosen priestess of the crawling chaos that is the Joker. The main reason that Harley is on the list is the full bodysuit she wears, that and being batshit crazy.

The Joker: The Joker is a foe of many potentials. On the low end, the Joker is a demented genius, sadist, and darkly charismatic leader. This Joker is basically Nolan's Joker. In the middle range, the Joker is a high power parapsychic, with mind control, emotion manipulation, and molecular conversion allowing him to pull comic props and weapons seemingly out of nowhere. On the high end, the Joker is the physical manifestation of a cosmic horror, a beast that previously dwelt in the space between realities. I would personally use this final option, but make the Joker a human vessel acting as the host for the cosmic horror that is the trickster god/monster Joker. Harley is his/its High Priestess, and the Joker's gang is more a cult than a criminal enterprise. 

Man-Bat: The Chiropteran Marauder (Human-Bat hybrid form) could be created with some creative and highly illegal biomodifications and genetic augmentations. This level of modification would certainly have serious impact on the sanity of the patient, such as largely losing the visible spectrum of light and entering into the realm of sonar based perception. To make a better foe, there could be a stock Man-Bat, and then there could be special forces trained Man-Bat or rogue parapsychic Man-Bat (strength, aura perception, etc)

Mr. Freeze: Cryonics are certainly a fun area for arcanotech R&D with gadgets like freeze rays, cryo-bombs, and other such ice and cold based technologies. Freeze would be an arcanotech engineer who spent too much time with his devices and has lost his sanity, becoming an avatar of cryogenic essences. Slap on a suit of power armor, a heavy cryo-beam generator and stay frosty.

The Penguin: Parapsychic ability is a fickle thing, and it works however it feels like working and is different from person to person. The Penguin's parapsychic ability manifests in a Dolittle like manner of speaking with animals, specifically avians. The Penguin is a mastermind rather than a fighter and has a mix of gang and mercenaries in his employ as well as a network of bird spies. 

Poison Ivy: Another unique parapsychic, Poison Ivy responds very strongly to plant biomass, and is able to control and manipulate it (Plant Adept?) to the point that she can integrate plant traits into her own body, including photosynthesis and creating toxins and compounds in her glands and skin. A very strong parapsychic, she is not just an environmental manipulator but also a seductress and a servant of greater powers (alien plant gods?)

Ra's al Ghul: Much like the Joker, Ras can exist on several levels. On the low end he can be the obvious mastermind and evil genius, pumping out exotic arcanotech weapons and gadgets (Lazarus Pit is a bioreactor) and leading a major corporation, or underground sect. On a higher end, Ras can be a walking avatar of cosmic weirdness and power, functionally an immortal mobile storm rift with impressive parapsychic abilities, able to enslave entire regions with the force of his will. (can also draw lines between Ra's and Yuri from C&C: Red Alert) 

Riddler: The Riddler has never been in my opinion a strong physical opponent. When Riddler becomes a rogue AI, it becomes much more interesting. Like the Puppermaster from Ghost in the Shell or any other hidden threat, the Riddler is a virtual threat, wreaking havoc through hacked machines and androids, and cyberrealm warfare. You didn't say the magic word, I want to play a game.

Scarecrow: A mind controlling parapsychic can easily specialize in causing and manipulating fear. Scarecrow takes it a step farther, forgetting to come back to normal and losing himself in the avatar of fear persona. The Scarecrow is a powerful parapsychic and unless sedated, can cause mass hysteria and manipulate fear across a large swath of terrain around him/it. 

Two-Face: Two-Face is the unfortunate recipient of multiple personality disorder. One personality is a relatively normal lawyer-y type, while the other is a deranged sociopathic killer. Fight Club style, both are aware of each other, and the normal one can do the normal things, while the sociopath has access to strong physical adept powers like enhanced strength and exotic manipulation of fate/movement of objects.