This has been suggested a fair amount and I have to disagree.
There was no incubation system before V2. The point of adding the system was to slow down the rate of hatches, thus putting fewer pets into the game and bringing pet worth up a bit. Soon after all of your eggs incubate, they're all ready to hatch as well. Which means that incubating all of your eggs instantly is just about the same as not having incubation at all.
If you really want all of your eggs incubated, you may take the time to do so. But if you think about it, all you really need to incubate is three each day. Pick out three (one if merchant) eggs every day to hatch the next day. Incubate those, hatch them the next day and then choose three more and incubate them. There you go, only three clicks per day and you always have as many eggs as you need.
In fact, I've heard many people say before that there should be a limit on how many you can incubate at a time, perhaps three or even one. I'd agree with something like this more because it would make the incubation system even more effective.