OK, so first off, I'm going to shamefully admit that I have not been using been using a
metronome for anything until very recently (About a week ago

). I've made feeble attempts in the past but it was unbelievably difficult for me to divide the beat at all, so I gave up. Recently I took the time to get used to it and I've already noticed big improvements in my playing.
Anyways, so yesterday I was like "I am going to work on my sweeping". I was planning on spending a solid hour (Yeah I have no life) on doing nothing practicing 5/6 string
arpeggios. So anyways I started doing them very slowly in, for example, e minor. I would stay in one inversion for a few times and then go to the next (because I don't want to get good at only one shape at one place, and it sounds much nicer and is funner for the fingers) and I very quickly noticed I was always screwing up on the 6 string ones in relation to the metronome.
I then realized that while you could divide the five string ones up nicely (6 notes up, 6 down, so triplets) for one beat, the 6 string ones have 1 extra note. that means that you would have 7 notes per beat if you wanted it to repeat nicely. You can't divide 7 notes further, and I can't do 3.5 notes per beat. Also, if your doing the whole motion in one beat, it really doesn't help accuracy because you undoubtedly will speed up some in the middle, or slow down at some places, and it simply doesn't work. it is even worse with the minor shape, because you have to roll your finger for 3 notes in a row.
The only way I've come up with that will easily divide into beats is this:

(accidentily put it in e major, whatever. You can do the same thing with major/minor)
The problem with that is you only go up the shape, and if you try to reverse it you will quickly notice it is very awkward for your fingers.
So I quickly checked youtube to see if its musical teachers of guitar would say anything anything about using a metronome. Obviously, there was nothing and I can safely say I am better than most of those guys trying to show off
Another related problem is to due with the natural harmonics on the 12 fret. That e minor shape is horrible because half the time you will have notes ringing out whenever you pass them. It makes good playing sound sloppy, and really sloppy playing sound better than it actually is (because you can more or less aim for the general direction of the 12 fret and that exact note will still sound). Now obviously I could just practice in a different position, but E minor is probably the most common arp ever used.
So, any suggestions?