This is a simple question and I'm hoping for some simple honest answers.

When playing scales, exercises, or three-note per string patterns, say like this:


Why am I supposed to use my middle finger for the second note? I struggle to do this ascending. Descending, I have less of an issue, but I believe that my hand shifts slightly allowing me to perform this descending. I've read I'm suppose to finger this particular type of patter 1,2,4, and I was wondering what benefit or reasons I have to stick with this and re-discipline myself to do it this way?
erhm, its more practical. Most people can stretch better between their 1 and 2 finger then between their 3 and 4.
my rule of thumb: if i can reach it with a finger, use that finger. this meaning, if im playing the above scale, i will play it index, middle, pinky. if it was say, the same scale at the 12th fret, i might play it index middle ring. its all a matter of comfort, however, but a very good practice especially to extend reach.
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Well to be honest its just the more proffesional and practical way to do it, theres tones of ways you could play it, i would say learn the correct way then feel free to play however it feels comfortable. Thats how i do it when im learning a song, i play it with the exact fingering, then learn it that way, and once i kno it i might change to whatever feels comfortable, which could be playing that with 1,3,4 or just whatever. Now im not much of a scale playing person, mostly because i play bass, but i still do some scales so i have a good grasp on em. But overall id say it like i said it before, learn it the right way then if u need to adjust go for it.
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erhm, its more practical. Most people can stretch better between their 1 and 2 finger then between their 3 and 4.

That's the answer.
Though Paul Gilbert likes to use his ring finger for the middle note in stretches like that. Just go with whichever's most comfortable to you.
If playing that pattern on frets 1-11, I use 1st, 2nd, and 4th fingers

If playing that pattern on frets 12-21 I use 1st, 3rd, and 4th fingers

But just play whichever way is easiest and more comfortable to you.
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Using the fingers 1 2 and 4 is more common than 1 3 and 4. Paul Gilbert uses the second method. It's not wrong as long as you're comfortable and the notes sound clearly.
You're not supposed to use your middle finger. You're supposed to do whatever the hell you want. A lot of people with an underdeveloped little finger would use index-middle-ring for it. That's the only one that would be classed as wrong, but only because you're intentionally limiting yourself.

Do whatever you want.
I think of it like this. If you were playing 6-7-9 then you would use index, middle, and pinky. When playing 5-7-9, there is now a stretch. Leave the other fingers in their "rightful" position and reach out/stretch with your index to get the note on the 5th fret. Stretch with the finger that is closest. Leave as many fingers in the "normal" position as possible.

Its more comfortable for me to do it that way. That's just my way of creating some reason behind it.
Do what feels best, but if this is an exercise it doesn't hurt to do it both ways. In "real" situations you are going to have to stretch between 1&2 sometimes, and between 3&4 other times, so why not practice both?