The proposal to use the current US59 route was for east Texas. It would make sense for I-69 to go around Houston to the west and connect with the current US59 southwest of Houston. That way US59 would connect with I-69 twice. Perhaps US59 going through Houston could be redesignated "I-69 Business".
“After a dozen town hall meetings, nearly 50 public hearings, and countless one-on-one conversations, it is clear to us that Texans want us to use existing roadways to start building the Texas portion of Interstate 69,” said Texas Transportation Commissioner Ted Houghton. “TxDOT’s recommendation would effectively shrink our environmental study down to roads such as U.S. Highways 77 and 281 in South Texas, State Highway 44 and U.S. Highway 59 along the Coastal Bend and U.S. Highways 84 and 59 in East Texas. We are dropping consideration of new corridors that would run west of Houston in addition to other proposals for new highway footprint in other parts of the state.”
http://www.dot.state.tx.us/news/017-2008.htm