When I trained myself to develop certain reflex actions, I used the alternate picking method. This meant down on 1 2 3 4 and up on the "&"s on 8th notes. On 16th notes, it was down on 1 & 2 & 3 & 4 & and up on the "e"s. I did this picking on any rhythmic configuration. For example & & & & would all be played up. This helped me a lot when playing or reading complicated rhythms. I think not having a picking system makes complicated rhythms harder to play. One of the biggest problems with not having a picking system is consistency. If I were to pick a pattern one way and have it sound fine, I might play it again with a different picking pattern. This would make the sound different and also might trip me up.
Nowadays, it is a different story. I am playing nothing but blues. No classical, no fiddle tunes, no jazz blowing. In blues, alternating picking can easily sound stiff and artificial. Instead, use hammers and pulls as part of my picking vocabulary. The result is much more personal and vocal. I remember a young Pat Methany, in one of his first interviews in a national magazine saying that he thought picking every note sounded "corny."
When I play my fastest patterns in blues, they are usually descending. If you listen to the greats, after a high climactic passage, they release the steam by doing a fast run down to a low note. It is kind of like shaking out a rub, or sweeping debris off a table with one sweep of your arm.
Technically, here is what I do. I pick every note when there are 2 notes on a string. I use alternating picking for these, with the downstrokes in sync with the "&"s as I described above. When I have 3 notes on a string in a descending run, I pick the first two notes so that they correspond to the rhythmic subdivision. The third note is a pull-off. If I do this on 2 or more strings, I can do it pretty quickly in a way that sounds more human and vocal than strict alternate picking.
I also use a lot of triplets in blues, more than straight 8th and 16ths. With triplets, I use strict alternate picking that results in having the second group of triplets picked the opposite way. I also use pull-off for the 3rd note on the string with descending runs.
Another picking method that I use is 1 starter pick, the have 12 or more notes played with hammer-ons and pull-offs. I'm working on raising my right arm up as I do this. Hendrix did this a lot and so does Prince. It is a great visual effect and very disoriented for the audience I would think. Runs that descend are better than going up because they are louder. Run going up have no pull-offs, just hammers.
Rhythm guitar is a very different animal, almost like a different instrument in some ways. One way is the strumming, which is rarely a straight up and down in sync with the beat. Playing that way is so mechanical. You have got to switch up the strum directions. A good way to practice is with a Latin rhythm book. I have seen in a book some rhythms that have up-strums on downbeat, etc. This was excellent practice for me. Strict downstrums are very common, as on power chords.