If you highlight the detective side of Batman, then I think it makes The Penguin and The Riddler much stronger villians. Show The Penguin as the boss at the head of Gotham's crime syndicate, and make the movie more of mafia movie. Don't make him an actual Penguin, or give him a Penguin army. Play him like a mob boss. For The Riddler, I think you could have some great scenes where Batman has to work his way through a guantlet of death traps. Don't just make The Riddler a comic vehicle. Play on his intelligence. You could make a decent horror movie with The Scarecrow as your lead villian.
If you're just going to have Batman punch his way through everything, then it limits your ability to have interesting stories with his villians. However, if you tailor the movie more to the villians style, it would give you a Batman movie that hasn't been done before.