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If you recall all the problems that Boeing has had with lithium ion batteries catching fire on the new Dreamliners, that may provide a clue to part of the reason. One of the places I order batteries from has an explanation on their website that pretty well sums it up:
"No, they are not available in standard sizes. We believe this is because it would be too easy for users to inadvertently put them in a charger not designed for Lithium-ion batteries creating a potentially dangerous situation. (If an alkaline battery is put into the wrong charger it might leak or even burst, but a lithium-ion battery put into a NiCd or NiMH charger not designed for lithium-ion, might ignite. Also, because Li-ion batteries operate at much higher voltage (typically 3.7V per cell) than the 1.2 to 1.5V of most cell batteries, designing a 1.5V lithium-ion cell would be expensive."