| I believe what he's asking is how to minimize the tonal differences between playing the same notes on different strings, e.g. and E on the 12th fret of the E string vs the 7th fret on the A string vs the 2nd fret on the D string.
The reason a difference exists is due to the difference in physics to create the pitch, namely thicker strings with a shorter vibrating length vs thinner strings with longer vibrating lengths. Also, there will be a physical difference in the location of peaks and nodes along the vibrating portion of the strings, and which peaks/nodes exist above the pickups (hope that made sense).
So anyway, to a certain extent you're never going to around it, so think about how you want the note to sound if you've got a real choice as to where to play it. Generally, use the thicker string higher up if you need the note to feel full. Use the thinner string if you want the note to be more biting.
You may want to post your question in the the strings forum, some string sets may be thought to have more equal balance string-to-string. I'd think that strings that are more close in gauge (say 90-75-60-50) might give more even response, but that could be at the cost of uneven tension (?), which is why I don't think such a set exists unless you buy singles - and I'd wager that road would be extremely hit-or-miss.
You can also experiment with adjusting pickup height, namely raising the pickups on the treble side to try to get more even response. | 
tonal transitions?? 
