In German, most of the time you try to avoid 'you' in academic papers. Of course I refer to 'you' in the meaning of 'in general' not you as a pronoun. What is the best practice in English?
Well, in scientific register, the "passive voice" is preferred rather than the active voice. Hence, if you take a look at credible scientific journals, you see there's no need to use "you", whilst in German you could use "man" and "passive voice" in scientific papers.
Man in German corresponds (in terms of meaning) to:
the English indefinite pronoun one (like doing one's homework). This is however more literary.
the English passive voice
It depends on who is meant by "you". If you are stating a principle which applies to anyone, such as:
You cannot simply ignore facts which you find inconvenient.
You can simply switch to the formal literary pronoun "one":
One cannot simply ignore facts which one finds inconvenient.
If though you wish to address the reader without seeming too familiar, you should address him in the third person:
The reader will readily perceive the chief flaw of this argument.