If we were talking about aerodynamic compromises made by Honda in the design of the first-gen Honda Insight, I can think of several: grille, underbody panels, the size of the car's trailing end, height and width of the car, and things that stick out into the airstream.
The biggest room for improvement is at the rear of the car. Foremost, the Insight needs a boat tail. Yes, it would be large and at times cumbersome, but if you need the best possible aerodynamics, you need a boat tail. I presume Honda omitted it for very good reasons. It would be hard to park a boat-tailed Insight in Japan and Europe, and possibly hard to sell such a car in America. There are also crash safety questions, namely: can you design a 5mph bumper that's 50cm wide? If you are rear ended at high speed, would such a boat tail act like a trench spike through the firewall of the guy behind you?
Notice how the bottom half of the rear is much less tapered than the top half. The rear track width dictates the width of the rear. I'm not suggesting you should move your suspension inward, but hey, it would improve CdA.
IMO, air should not travel through the engine bay, except as required by the radiator. Honda's gasketed hood and engine bay underpaneling are good, but both can be improved on slightly. A more complete engine bay cover increases the cost/hassle of servicing the vehicle. If you complete that and a grille block, you may want to reduce the size of the engine bay to wheel well passage too.
There are a few simple appendages that hang out in the airstream. In order from largest CdA to smallest: wing mirrors, rear wiper, door handles, antenna, washer fluid nozzles (x3), raised hood emblem. Some of these things are very necessary on a road-going car, while others were added to conform to regulations and/or consumer expectations. Of these, I've only removed the rear wiper, and I plan to remove the mirrors, antenna, and one washer nozzle.
Frontal area reduction would help. I could still seat two side-by-side with a few inches less overall width, though it would be uncomfortable when large people are in the car. Likewise, the roof could be lowered by reclining the passengers more or excluding tall people.
The Insight has 5.9" of ground clearance. A lower design would reduce CdA, though lowering the car yourself is not guaranteed to do so. I would favor more aggressive fairings in front of and behind front and rear tires, even though they'd likely come in to contact with pavement at some point.
The Insight leaves the factory with an excelled Cd=0.25. I wonder if 0.20 or even 0.17 is within the reach of an EcoModder.