First of all, mini guitars are notorious for bad intonation.
The most important step to obtaining a 'harmonious' guitar (ie one that plays in tune all over the neck) is a good setup.
Theses are the main factors that affect how 'good' a guitar sounds (tone aside):
Nut height- nut slots that are too high will cause the first few frets to sound sharp as the strings are further from the frets they require more force which increases tension and sharpens notes. Nut slots that are too low will produce fret buzz when open strings are played.
Intonation- Each string must have the correct length to play in tune up the neck. As each string is a different thickness each individual string will require a different adjustment to achieve this correction.
Action- Effect is similar to nut height but applies to the entire neck, high action will require more fretting force which increases tension and sharpens notes. Low action will produce fret buzz.
Neck relief- The forward bow of the neck which allows for the greater amplitude of the vibrating string at it's mid point. Affects all other areas.
All of these things are interrelated and compromises must be made eg lower action will improve intonation but will increase fret buzz and decrease sustain.
There are myriad other factors but those are the most important.
A more expensive guitar does not necessarily have a better setup, Gibson are well known for having poor setups on $5k guitars. Most guitars in stores have not been set up at all bar minor adjustments at the factory.
Your best bet is to chose a guitar you like the look and tone of and take it to a reputed luthier and get it setup for your intended purpose, a good luthier will know how to set it up best for you based on your style and technique.