The syntax is this way in this type of sentences. It's like saying "The (act of) waiting is difficult" or "The waiting thing is difficult".
To turn the verb into a noun-ish thing which can be a subject of είναι δύσκολο.
English has a gerund "waiting" which is a noun meaning "the act of waiting", but Greek doesn't have something like that.
You can form related nouns from some verbs such as η παραμονή from περιμένω, but that is more "the stay" than "the act of staying/remaining/waiting" -- I think you'd use it more in sentences such as "I had a nice stay".
So you end up with constructions like this one which are literally something like "the [fact that] you wait".
Mizinamo (or Troll or anyone else), would you be able to answer a question for me? For gerunds, is the bit formed from the verb always given in 2PS, ie περιμένεις, διαβάζεις, τρως? I would have thought it would have been formed from the third person singular but that doesn't seem to be the case here.
It depends on the hypothetical subject.
You can say Το να περιμένω είναι δύσκολο "Waiting is difficult" if you want to say that it's difficult for you -- like "Waiting is difficult for me" or "for me to wait is difficult".
Or Το να σε πιστεύει κανείς είναι αδύνατον "Believing you is impossible", literally, "for someone (κανείς) to believe you is impossible".
The second person singular as here seems like generic statements in English, where things such as "you can't see Everest from here" doesn't literally mean "you, the person I am speaking with right now".
This construction is not really a grammatical concept the way "gerund" is in English; just a nominalisation of a clause, and the subject of that clause can be anything convenient -- second person singular is not the only possibility.
Isn't "περιμένεις" related to "you"? So I put "Your waiting is difficult" (formal English), but it was rejected!...
Because it follows 'Το να...' it's meant as a general statement, not a personal 'you', despite its ending. So the most appropriate translation is just with the gerund in English. You could also say 'Το να περιμένει κανείς', which is the equivalent of 'when one waits...' which is also obviously a general statement and not a personal third person statement. :)