I was hoping the Gen 2 was the one for me, but after comparing the numbers, it seems Gen 1 is still the better choice.
On the web, I've seen guys make a floor kit with a tire chock that makes a bike fit between the seats of the Gen 1.
Transit gen 2 measurements
http://www.ford.com/trucks/transitconnect/specifications/interior/
Rear door opening width at floor: 49.3
Rear door opening height: 44
Load floor height at curb weight: 23.4
Cargo length at floor: 71.5
Cargo width between wheelhouse: 48.3
Cargo length at belt: 61.3
Cargo height maximum: 49.7
Transit gen 1 measurements
https://www.fleet.ford.com/truckbbas/topics/2012/12_TransitConnect_SB.pdf
http://www.iseecars.com/car/2012-ford-transit_connect-dimensions
http://www.ford.com/services/assets/Brochure?make=Ford&model=Transit%20Connect&year=2012&postalCode=92602
Rear door opening width at floor: 50.2
Rear door opening height: 52.1
Load floor height at curb weight: 23.1
Cargo length at floor: 81 (at floor, seat back to rear door)
Cargo width between wheelhouse: 48.1
Cargo length at belt: ?
Cargo width at belt:
Cargo height maximum: 53.7