How to avoid Apple Pencil 2nd Generation battery failure?

You might have to accept the first failure, because battery failure after allowing it to become deep discharged is pretty much operator-error. It also sounds like it was too long ago for a possible warranty claim.

Your description of the second failure sounds more like a possible warranty case if it failed after only 6 months. However, you would probably need to make your claim within the warranty period (probably 12 months after purchase). You know the dates, and will have to judge whether that is still possible. If you think you might have a case, contact Apple support and discuss with their support agents. As minimum, if you are buying the replacement in person at an Apple Store mention the problem to the store team and ask if they can help.

Without detailed knowledge of precisely how you use and/or maintain your Pencils, it is impossible to provide a definitive assessment as to why you have experienced multiple failures.

Some end-users, such as yourself, suffer repeat failures. Others users have Pencils that continue to function flawlessly for many years. Speaking of personal experience, I am in the second category; I have both a first generation Pencil (+6 years) and a second generation Pencil (+3 years) that continue to operate and perform entirely as expected.

Being entirely objective - setting aside the possibility that you have just been really, really, unlucky - you might reasonably consider that something about your usage is potentially the cause of a shortened lifespan.

All iPad Pencils have a one-year limited warranty. Baring physical damage, should the Pencil fail with its warranty period, Apple generally replace a defective Pencil without question.