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As someone who works on stop/start systems, there are a variety of reasons that people don't like them. In short, they are as follows:
1. Loss of certain power assistance features. On cars equipped with hydraulically assisted steering/braking systems rather than electrically-assisted ones, turning the engine off often means losing those power assistance features.
2. Loss (or weakening) of certain comfort features such as A/C, and the like.
3. From the engineering side, one of the major problems is the NVH caused during start-up/shut-down of the driveline. Furthermore, because of the manner in which ICEs function the combustion cycle may stop at any number of different positions during an auto shut-down. As a result, the engine may effectively be flooded in one or more cylinders, it may have an incomplete combustion event on auto-start, and so on. The results of each of these is a lag in start-up and significant NVH.
Depending on the software controls, some of these effects can be mitigated, but frankly, because there are only so many things you can do to speed up an ICE's starting procedure, there will always be some additional NVH and/or lag between start-up and the shut-down state.
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