The section between Indianapolis and Evansville is controversial. There are two options here:
1) Build a new alignment, partially upgrading Route 37 on the spot.
2) Upgrade Route 41 south of Terre Haute to a freeway, and use Interstate 70 from Terre Haute to Indianapolis as part of I-69.
Option 2 is something like eight miles longer, and is greatly preferred by environmentalists. Option 1 however provides access to Bloomington and the Naval Surface Warfare Center Crane Division.
There is also some question as to whether the whole route is needed or is simply pork; it is worth noting that, once you get out of northeastern Texas, a fully-Interstate route is available to Port Huron that is slightly shorter than the proposed I-69 routing.