One of the things I dislike about hybrids over diesels is the battery factor. I know batteries have come a long way, but they will still have to be replaced, and it will cost a decent amount. At what point is battery replacement going to cost more than the car itself? I guess that's more financial/environmental(throw-away car) than engineering, but it's the engineering that creates the issue.
Another (albeit not a big deal) thing that bugs me is the hybrids generally have uber-skinny tires and are relatively light cars to begin with when compared to say a VW TDI. I think if you could take one car, and try both options(diesel and hybrid), you would have two cars that drive very differently, but have about the same performance(in terms of power and mileage) with perhaps a slight advantage to the diesel when it comes to passing power.
Then you have cars like the Accord hybrid- it can shut down certain cylinders when cruising to save fuel, and the engineers used new weight-saving techniques in the car to make up for the batteries... so why not do that for ALL the cars, instead of just the hybrid. You have a car that is significantly more complicated than a normal Accord, gets maybe 25% better mileage, and a lot of that improvement is from non-hybrid engineering.
Ok, moving on... this one is hard for me to put into words, so bare with me.
A car has a certain kinetic energy when moving, which is either lost through heat when you brake, or in a hybrid is captured by the regenerative braking. But to me, that sounds like you have to drive inefficiently to make the hybrid work at all! If you want to drive efficiently, you drive so that you avoid braking completely.
Taking off from a green light, with another stop light one block away. In a hybrid, you accelerate and then have to hit the brakes and come to a stop at the next light to save/transform some of the kinetic energy the car had.
In a non-hybrid, you just accelerate more gently, or perhaps at the same rate but to a lower speed. So the next light turns green before you get there. Ideally you don't have to brake at all, so you maintain all of your kinetic energy.
If you drive a hybrid that way, you're not using the "hybrid" at all, you're just driving a car with a tiny engine.
To me, a hybrid sounds like a crutch for wasteful driving, not a wasteful powerplant.