Wow, two totally different cars at opposite ends of the Lexus lineup. Interesting that both are being considered and I can only imagine it's due to a 35-40K$ budget.
Besides what lexuslover stated and personal design/styling preferences your wife may have, other things to factor in. If you value prestige and knowing you want the vehicle that has won the most #1 quality and reliability awards since 1989, look no further - get the LS. It is known for the highest levels of automotive craftsmanship, reliability, fit-and-finish, materials quality, noise levels, ride quality, and so on. Here's just one very recent one, of hundreds of awards, won over the years: http://lexusenthusiast.com/2013/06/1...quality-study/
The LS will also have available options to coddle you that the CT doesn't have:
pre-collision, VDIM, BSM, self-parking, rear and side sun shades, self-closing trunk, wallet key fob, heated steering wheel, power tilt and telescoping steering wheel, dynamic radar cruise control, top-notch sound systems (i.e. ML), rear DVD, and the list goes on...
The CT's biggest advantage is its operating costs.
It will be much cheaper than the LS. Besides fuel costs of at least 60% cheaper for the CT (regular vs premium and 40+ mpgs vs 20), its maintenance costs will also be similarly cheaper especially if you service it at a Toyota dealer (it's mostly a Prius mechanically). I wouldn't service the LS at a Toyota dealer as there is no equivalent Toyota model...
As a nearly 2.5-year owner of the CT, believe me, the CT is a fantastic commuter city car that is cheap to operate, fun to drive and easy to park all with a sporty style to it. Ride is a little firm and somewhat noisy (for a Lexus), but acceptable. However, if operating costs were not a factor to me, without a doubt I would be choosing the LS over the CT as I value craftsmanship, luxury, and heritage. There is no comparison.
Good luck and keep us posted! This is really an interesting set of choices.