Joined: Aug 2010
Posts: 12,711
Likes: 2,100
From: Madison, WI
Bikes: 1961 Ideor, 1966 Perfekt 3 Speed AB Hub, 1994 Bridgestone MB-6, 2006 Airnimal Joey, 2009 Thorn Sherpa, 2013 Thorn Nomad MkII, 2015 VO Pass Hunter, 2017 Lynskey Backroad, 2017 Raleigh Gran Prix, 1980s Bianchi Mixte on a trainer. Others are now gone.
The net difference in elevation from start to finish is the same. Thus, if the hilly route involves a lot braking and the non-hilly version does not, the braking is all extra work that you did on the uphill and wasted as heat in your brakes in the downhills.
On the other hand, if you did not need any braking on the downhills because the slope was flat enough, the work would be similar.
This assumes windage and road surfaces are not considerations, comparable traffic, etc. I am neglecting the fact that speed and work are not a linear correlation. Generically, I would pick the flatter option if all other factors are equal.