Possibly the most (in)famous examples of aftermarket li-ion replacements for either ni-cad or Lead-acid batteries are those of aircraft. There were many problems for nearly a decade, related to charging protocols, discharge protections/protocols, and battery design. There is copious documentation on these issues from NTSB hearings (I attended them on behalf of one manufacturer) and specific application failure events.
There is zero question that simple plug-replacement of one type vs another, even one specific li-ion chemistry vs another, requires modification in use procedures. We all know that, for example, Tesla has different charge protocols, different tapers, based on series of battery.
As for replacing the lead-acid 12v in our Model S with anything else it be hooves us to avoid simple generalization and understand that all, repeat all, the 12v systems on the Model S are automotive standard designed for use with 12v lead-acid. Even major auto manufacturers have not yet managed to switch to anything else despite obvious overloading of 12v systems. There has Benin major effort to move to 24v or 48v or even higher that has not happened mostly because of the cost of change and burden of non-standard approaches. Tesla does not have enough scale to fight that battle.
Among the aircraft, marine and other applications that use more appropriate electrical standards all of them are very, very expensive and are not well-adapted to large scale. These will reach automotive use, of course, but if Tesla goes there before there is industry scale all our standard switchgear, pumps, lights etc will suddenly become far more expensive and difficult to source. Bad idea, fir now.
I'd love to see li-ion as the low-voltage solution but there is zero chance I'd install an aftermarket solution without comprehensive knowledge of total design, production, testing, etc. if anybody thinks otherwise just look at, say, Cessna aftermarket success and Boeing 787 lack of testing and qc.
I know now this is a good idea. Doing it properly is a Big Deal. Ain't no game for a hobbyist! At the minimum think voided car warranty. Very possibly think fire.