What do you mean by regular scales? Pentaton? For me 3 note per string is the "regular". It is THE full 7 notes of a Key. I think you should learn it because once you get into modes and stuff that is when you will sing real melodies on your guitar. Like Syn. Also for me playing fast 3 per string( diatonic) scales is more comfortable then fast pentaton up and down.
It indeed wasn't that hard after all. I tried to go through all the modes 3nps without a paper in front of me yesterday after I posted this and I actually could do it. Knowing the notes in the scale helped, I couldn't visualise the pattern out of mind.(Which I like for some simple mindless improv)3 notes per string is important IF you want to economy pick. The weird thing about them is that you end up in a different position than where you started. I don't economy pick that much so I prefer the old school way where you stay in one position. You should really know both. Once you know the regular way, it's really not that hard to switch to 3NPS.
My opinion: it's just notes. I don't see how anyone could think exclusively in one or the other. It's easy to find obvious cases of both being used in the music I like.
The thing about music is Technique, Theory, and actual Music are all an inseparable blob. It's basically impossible to look at any one of those in isolation without the other two. If you learn a lick or a solo that's music played with techniques within what is probably a scale shape. If you like 3nps but then you learn a song which was written and works better the other way, then you're doing it the other way. Even if you play straight up and down a scale you're developing good or bad technique as you do it, and maybe you're also unintentionally learning Slipknot's "Nomadic".