I read somewhere that the B-1B's Achille's Heel was a weak airframe.
Since it was orginally designed to be a long-range strategic (nuclear) bomber, they gave it an airframe that was adequate for a few, long, high altitude missions. The B-1B's use as a tactical bomber and for close troop support stressed its airframe more, and in ways, it wasn't designed to accomodate. Frequent lower altitude missions casued the airframe to age out early.
If the B-1B had a durable airframe like the B-52 and the B-2, it would have a longer service life.