[Ecky]

I've been thinking about this for a while... I believe the VTEC mechanism in Honda's R series puts the engine in Atkinson cycle when cruising, and changes back to Otto when idling or accelerating. It would surprise me if modern engines from other manufacturers didn't already do this.

It would probably be simpler to use one of these engines since they are already tasked for what you want, though you'll probably pay more for the engine. The only issue I see is, the smallest R- engine you can get in the states is 1.8L, which is more than overkill for the eco-minded. They have a 1.6L variant in Europe and Asia but you'd need to import one.

The only manual transmission Honda makes for the R18A is rather short, since they're marketing manuals as sportier.

You would see MPG gains over a 2006+ Civic so long as the vehicle you dropped it into was lighter or had a lower CdA, such as a CRX. It would also be beneficial to mate it to a longer transmission, like that found in the CRX HF.

I'd also definitely do some research to see if the ECU could be reprogrammed to increase the variety of conditions under which it goes into Atkinson cycle, and also whether you could map it for lean-burn. (The R-series fuel mappings are more focused on emissions)