Part - or most - of the loss in charging and discharging batteries is due to internal resistance. This is converted to heat, which is why batteries get warm when being charged up. The lower the internal resistance, the better.
Slower charging and discharging rates are more efficient. A battery rated at 180 amp-hours over 6 hours might be rated at 220 AH at the 20-hour rate, and 260 AH at the 48-hour rate. Much of this loss of efficiency is due to higher internal resistance at higher amperage rates - internal resistance is not a constant - kind of like "the more you push, the more it pushes back".
Typical efficiency in a lead-acid battery is 85-95%, in alkaline and NiCad battery it is about 65%. True deep cycle AGM's (such as Concorde and Deka) can approach 98%.
Practically all batteries used in PV and all but the smallest backup systems are Lead-Acid type batteries. Even after over a century of use, they still offer the best price to power ratio. A few systems use NiCad, but we do not recommend them except in cases where extremely cold temperatures (-50 F or less) are common. They are expensive to buy, and very expensive to dispose of due the the hazardous nature of Cadmium.
We have had almost no direct experience with the NiFe (alkaline) batteries, but from what we have learned from others we do not not recommend them - one major disadvantage is that there is a large voltage difference between the fully charged and discharged state. Another problem is that they are very inefficient - you lose from 30-40% in heat just in charging and discharging them. Many inverters and charge controls have a hard time with them. It appears that the only current source for new cells seems to be from Hungary.
An important fact is that ALL of the batteries commonly used in deep cycle applications are Lead-Acid. This includes the standard flooded (wet) batteries, gelled, and AGM. They all use the same chemistry, although the actual construction of the plates etc varies.
NiCads, Nickel-Iron, and other types are found in a few systems, but are not common due to their expense, environmental hazards, and/or poor efficiency.
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