Make sure any re-used beams are straight. They're often not, and they can't be forced straight like a 2x. If they have mortise cutouts (most do, unless they're from a barn), you'll have to decide if they'll look odd where you're placing them. IMO re-used beams look best when they look like they may be in their original location. Look for insect infestation. Little round holes in the surface could be a sign of powder post beetles, which is very common. You may need to treat chemically, or I hear freezing works. If you want natural look, just clean up with soap and water and dry.

A whole lot of real beams holding up real houses aren't straight, or anything like it. It's part of what makes them look not fake. Your timber framer should understand how to deal with them.