I'm not convinced that the Elise is an S2000 killer. Sure, it crushes it in performance, doing everything the S2000 does, only better... but a lot of people just want a sporty roadster, and the S2000 is a lot more practical for most people. It's easier to get in and out of, and when the top is down, it's REALLY down, not just the targa. It's a lot more of the open air feel. It's got a nice interior, good handling, and plenty of acceleration. It's also sold in greater quantity than the Elise, making it a little easier to get ahold of.
That being said, the motor is the biggest selling point for that car, and I could see that putting it in the elise could hurt their sales a bit. But why not the K20C? It's Honda's second best motor, it would fit the character of the elise, it is easy to tune, and it won't detract from the allure of the S2000.
While on this subject, though... Ford really dropped the ball by not getting one of their engines into the Elise. I don't mean that as a consumer, I mean that from Ford's marketing standpoint. They are trying so hard to play up the heritage of Ford right now, what with the new mustang and the GT... and they totally threw away a chance to bring in echoes of Jimmy Clark and Lotus-Ford.
They could have had some great marketing for relatively cheap.