I agree, I don't think he could pull off the look like Owen, Butler, Fillion, or Bana could. All those guys have a rugged look, well at least Owen, Butler, and Bana do. Fillion I've never seen look weathered or grizzled, he's usually always pretty polished.
Owen, Butler, and Bana routinely rock the 3 day beard growth and wear it well. Not to mention they all seem to inherently have that tougher edge, that Indy needs to have. Bale is a fantastic actor, but Indy wouldn't be the best fit for him. He's great though at darker more complex charcaters like Batman, Patrick Bateman, The Machinist, etc..