In my opinion, I would have to say the Gen 2 is superior to the Gen 1 for many reasons. I'll discuss a few topics.

Fuel Economy. Although the database shows the Gen 1-MT beating the Gen 2 by 1mpg, you should consider a few things. The Gen 1-MT numbers are mostly from cars that are broken in and from drivers experienced in driving a hybrid. The Gen 2 numbers are more weighted towards low mileage vehicles (not fully broken in) and new hybrid drivers. There is no way to quantitate this, but I would guess that these factors would be more than 1mpg. The only scientific comparison, that I know of, of their fuel economies was done by the EPA. Everybody knows that these numbers usually do not translate to real world driving, however, they are each tested in the same manner. This makes it scientific. The EPA gives the Gen 1-MT and the Gen 2 a 46/51 and a 49/51 city/highway mpg rating, respectively. The Gen 2 is better. My personal mpg is near the EPA rating. I'm sure I could do better, but I use AC when it's hot and I drive it even if it is just a short trip. The alternative would be to drive my minivan on short trips to artificially boost the FE on my Civic. This would help me win a "game", but it would defeat the true purpose of having a hybrid. A hybrid saves gas even if a trip doesn't allow it to beat the EPA numbers.

Power. The Gen 1 has 93HP (85 gas & 13 elec.) and the Gen 2 has 110HP (93 gas + 20 elec.). At first glance, the newer Civic is 17HP or about 18% more powerful. However, the Gen 1 was measured using the old SAE method and the Gen 2 was measured using the revised SAE method. For comparison, my 2005 Honda Odyssey measured with the old SAE method was rated at 255HP. The 2006 Honda Odyssey (identical engine) measured with the revised SAE method is only 244HP. Anyway, the Gen 2 engine is probably about 25% more powerful than the Gen 1 engine. I'm not totally sure how this translates to actual speed numbers, but I'm guessing the Gen 2 is "faster." The faster the car is, the less likely you will need a special "fast" car. This will further reduce gas consumption and emissions.

shelman also made some good points about safety and comfort advantages of the Gen 2.

Seriously, I have nothing against the Gen 1. I picked the best available car for me at the time I was in the market for one. I also know there is a chance that I will be jealous of future hybrid models as they come out. To expand on what shelman said, just as the Gen 1 helped pave the way for the Gen 2, hopefully the Gen 2 is paving the way for an even better Gen 3.