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Even absent the replenishment concerns, the amount of height and/or volume for gravitational storage just isn't practical. A kilogram of hydrocarbon fuel has ~40MJ of contained energy. To store the same amount of gravitational potential energy in a kilo of (water, but really anything) requires lifting it 4000km.
I'm not familiar with the state of the art in biochemistry, but the energy density of hydrocarbon fuels would plausibly make them excellent storage if we could produce them (from non-fossil sources) with even moderate efficiency. Not to mention the existing infrastructure. That said, that is a nontrivial synthesis problem.
Gravity storage with water as a medium is actually quite practical, and there are plenty of operational sites already, some with GWhs worth of capacity. You don’t have to lift 1 kg of water 4000 kms, you can instead lift 40 000 kg of water by 1000 meters.
This is practical and done in production, the problem is that you need a lot of water, and a lot of space to store this water in two separate reservoirs, which also need substantial difference in altitude. Because of this, it simply doesn’t scale: good sites are already mostly used, and we can’t build many more.
Synthetic hydrocarbons would make excellent store of energy, being very dense and already integrated in existing economy. The problem with those, though, is that the round-trip efficiency is really bad.
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We already can do something similar to this by producing hydrogen gas from water. Hydrogen has an energy density of about 33MJ/kg, which is comparable to hydrocarbons, and production is relatively trivial. The problem comes in converting it back to usable energy, which requires complicated fuel cells that are relatively expensive, which is, I believe, the biggest reason why the simpler but inferior EVs got the edge on hydrogen as the "green" vehicle solution.
Hydrogen isn't currently a panacea: it's difficult to store long term: it isn't very dense at room temperature and liquefies at a difficultly-low temperature. It also likes to leak really easily.
I don't know that it can be made practical for vehicular applications, but if you're thinking about fixed energy storage infrastructure it's probably worth considering.
Converting it to methane, if you could do so scalably and efficiently, would make the longer-term storage problem (months) much easier.
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