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I think the use of Hydrofluoric Acid was script-driven rather than fact driven: it sounds scary rather than being a good choice. Also, it allows for the possibility of the darkly comic bathtub scene where the acid dissolves a ceramic bath because Jessie ignores Walter's instructions (which establishes Walter's expertise and Jessie's lack of it).

There is no good reason why Pinkman and White pharmaceuticals needed to have hydrofluoric acid, therefore using large quantities of it is somewhat implausible.

Moreover, it probably wouldn't work as well as several alternatives. Hydrofluoric acid is very nasty stuff, but it isn't a strong acid. Even when dilute it will etch glass and ceramics, but it won't dissolve or burn flesh. I once saw a demonstration where a lecturer showed this by spilling some dilute hydrofluoric acid on his hand and then onto a glass surface. The surface was frosted, his hand unharmed (he was very careful to wash the acid off quickly and take appropriate precautions and I don't recommend trying this at home!)

Its danger to people is its toxicity, not its ability to burn: it insinuates itself into the body and destroys connective tissue and bone slowly by interfering with anything containing calcium. Its danger is worse because it doesn't cause immediate damage and you may receive a dangerous dose without noticing. So it is scary but not corrosive.

Other alternatives are better. Concentrated alkalis such as Sodium Hydroxide are readily available and are very good at dissolving flesh (which is why they are commonly used as drain cleaners). But alkalis don't do a good job on bone. Concentrated sulfuric acid is even better as it does a good job on flesh and will, eventually, dissolve the bone as well. Murderers have used both methods to try to dispose of evidence. For example, John George Haigh who used sulfuric acid and left little other than gallstones (http://en.wikipedia.org/wiki/John_George_Haigh). Using alkali is often done but tends to leave bone fragments even with sophisticated processes that pressure cook the solution (see http://www.slate.com/articles/news_and_politics/explainer/2009/12/soluble_dilemma.html).

So I think the answer is that HF solutions are not a good choice for body disposal as it probably doesn't work well compared to known alternatives.

Update

A lot of the above is theory but good scientists do experiments. So Periodic Videos decided to test this very idea using chicken legs as a model. They compared what happens when raw chicken legs are suspended in strong solutions of HCl, H 2 SO 4 and HF. The HF was the least impressive for flesh-dissolving characteristics, though it did seem to cause other, more subtle damage, to the components of the flesh.

See the actual results here.