A fact of life for guitarists: most of the world’s guitars do not play in tune. Classical guitars will always need lots of tuning just because of the vagaries of nylon strings. Many guitarists, however, expend much more time and effort tuning their instruments than should be necessary, and they often blame “bad strings” for their troubles when the real culprit is the guitar itself.
There are a number of reasons for poor intonation in guitars. The spacing of the frets may be inaccurate. (Some of the worst offenders on fret spacing are individual guitar builders whose work may be otherwise estimable.) The fingerboard may be distorted: backbow, or too much forward bow, or a crook at the 12th fret. The most important reason why guitars don’t play in tune, however, is that the scale length is not properly compensated. Compensation for intonation means adjusting the string length to deal with the fact that pitch changes because of stretching the string when fretting.
My classical guitars are all made with built-in advanced intonation features to make them play in tune anywhere on the fingerboard. The technical details of my strategy are covered in my article Intonation.