Since we just had a trilogy of Batman films that were a lighter on the supernatural/fantasy side of the mythos, I'd like Reeves to steer his film/s more towards that direction.
I've been thinking about some angles Reeves could take, and the villains that fall under them:
The "monster" movie
Pretty self explanatory. This movie would deal with a mystery with a monster at its core. The obvious choices are:
Basil Karlo/Clayface
Kirk Langstrom/Man-Bat
Waylon Jones/Killer Croc
I think Croc works best as a hired thug, so I'd rule him out. Between Clayface and Man-Bat, I would give the edge to Clayface. While Clayface has supernatural elements to him, he is not nearly as heightened fantasy as Man-Bat is, so he might prove the more palatable concept.
The "occult" movie
This movie would deal with a mystery involving cults, devil-worshipping, and/or the existence of spiritual evil. Something along those lines. Characters that fall under this category right off the top of my head:
Brother Manfred
Deacon Blackfire
Simon Hurt
This is where things get a bit tricky, because now we are getting into very obscure Batman villains here. Blackfire and Manfred are one-off characters appearing in graphic novels, and Simon Hurt is a fairly new addition to the Batman mythos. I wouldn't want Reeves to do a straight adaptation of any graphic novel, so unless he came up with a new story for Manfred, I'd rule him out. I was originally leaning towards Blackfire, but him being the leader of a fanatic cult lurking in Gotham's sewers may be too similar to Bane and The Dark Knight Rises conceptually. So again, unless they changed things up a bit with Blackfire's plot, I'd rule him out too. Simon Hurt seems a good fit here.
The "haunted house" movie
While I would not want a straight adaptation of it, I would love to see a film inspired by A Serious House on Serious Earth. Arkham Asylum has been sorely underutilized on film. It is the "heart of darkness" in Gotham City. It's an old institution with plenty of legends, stories, and superstitions surrounding it. Not to mention the evils that lurk within its walls. I'd very much like a movie where Batman has to solve a mystery inside the asylum. Also, because you have an opportunity to have cameos from Batman's more iconic villains, you can afford to go a bit more obscure with the main antagonist. Any of these would do:
Dr. Cavendish
Hugo Strange
Jeremiah Arkham