You seem to have several misconceptions. ‘thou’ is an archaic form of singular ‘you’. ‘Thy’ means ‘your’.
Archaic conjugation was also different than modern conjugation. A few of these are known today such as ‘hast’ or ‘dost’ because they appear in literature or the Bible. But even though these archaic forms are not well known, ‘thou wish’ sounds very wrong. If you had to use an archaic form, and you probably don’t, you should say something like ‘As thou wishest’.
‘As you wish’ itself has a somewhat old-fashioned, but not archaic, sound. To my ear, it’s kind of formal and British. It has several different meanings depending on the context. It can convey reluctance, as another respondent noted, but also respect or submission. (It’s your wishes that matter and I’m here to fulfill them)