You sound like you have a pretty mechanical approach to this, it's music, it's meant to sound good.
Open strings ring a lot more they have more zing and more sutain.
Fretted notes sound more punchy and bassy.
What is going to sound good in that particular passage in the song?
it's up to you, play what fits the song.
It might sound mechanical, but if it stops me getting an RSI then it's all good. I was merely suggesting an economical alternative. Ofcourse there are tone differences, but there are tone differences between chosing between the same note on different strings anywhere on the neck, if for instance you play an open G, fretted G on the D string @ V, a fretted G on the A @ X, and a fretted G on the E @ XV they all sound completely different. Yes there is a matter of choice between sound, but there is also a logical position to play a note as well. For instance if you approach it with an upright bass hat on then you'll start thinking that you can't physically reach a note in a certain position, so you might need to play an open string. A great example would be the bass melody in So What, which can be played in a number of positions with open and/or closed notes. You can start on an open D (or a fretted D fret V/A string) and move to a fretted G fret V, playing the melody in fifth position. Alternatively you could use the open notes D & G, playing the rest of the melody starting in II and shifting up the G string. Each has a different tone, but it is easier (for me anyway) to play the entire melody in one position. This also means when I play it on an upright I don't have to move my hand quite so much and hold a better intonation between the notes, rather than having to shift position.
But like you said, the genre, style in which you are playing, physical sound of your instrument, and other things come into it as well. If you know you have a deadspot on the G, then you might try and avoid that. Or if you know that it will sound better played entirely on one string then that could also be better.
Hope there are some useful tips there.
let us know how you get on, or if we've confused you too much.