Many reasons, when my 360 pad dies, I walk 3 feet over to the wall, pull out 2 more eneloops, and continue. With the ps3 you're required to be tethered to the console for X amount of time until you finish charging it, and it came with a 1 foot USB cable. You then have to deal with the long term issue of the charges holding worse and worse and of course outright dying in the future. I have 3 PS3 pads and none of them have crapped out yet but, when they do, it's going to be a much bigger hassle to take care of. And don't tell me how you can by a USB cable for a few bucks, because guess what, that's how much multiple eneloop batteries end up costing.
In the end, the cost of rechargeable batteries that are also universal means the controller can in theory last forever until you outright break it, so while I won't condemn Sony's approach, as someone who likes to whip out vintage consoles from time to time, I do prefer this. It's ultimately cheaper to handle it this way anyways, My Wii remotes, 360 pad, remotes for the tv, other devices, I just buy a pack of eneloops cheap on amazon and keep a set on the charge. People who prefer the lithium method are either bad shoppers or short sighted in my mind. I'm not sure what kind of battery the PS3 pad uses, but is it a universal style that i'll be able to buy with a perfect charge in 10 years?