doing finger exercises but i notice when i play 3 notes per string, like down up down up down up... it'll go like this:
E: down up down
A: down up down

see, it's not really alternate because it should be
E: down up down
A: up down up

is this a big deal? and will simple practice fix this?
You should strive to alternate pick correctly. Practise will indeed fix it, after a while it'll become second nature to alternate pick.
Speed is a by-product of shut the fuck up.
sounds like you are economy picking, which is a good technique to know, you could probably read more about it on some of the lessons here
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What you're doing is actually economy picking, and if you embrace it as such, it will be even easier to play.
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it depends what you're doing between strings.

If the adjacent downs are done in one stroke without a pause, that's economy picking and it's fine.

If, however, you are doing them as two seperate down picks, that's bad
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so when it comes to speed, it wouldn't be a big deal? i've always called it economy picking and i kind of prefer it because it feels more natural, but i was a little afraid it might have a negative result on my playing in the next 1~2 years.
I can almost guarantee you're not economy picking properly. As pigeonmafia said, economy picking involves taking the two consecutive downstrokes (or upstrokes) in one motion, it isn't something that you generally learn by accident.
I would very much recommend focusing on strict alternate picking (upstroke ALWAYS follows a downstroke and vice versa), at least for now. If in the future you want to develop economy picking, go for it.
Speed is a by-product of shut the fuck up.
I did this for the first year I played. I economy picked. It just came naturally that way. It sounds really smooth and fluid when you change strings, but it just doesn't work (or feel right to me at least) for some things.

The biggest problem I had was that I economy picked when I ascended but not when descending.

Practicing strict alternate picking for a couple days eliminated it. Now I have to really focus if I want to economy pick.
i've had the same problem.. Solution: technical difficulties by Paul Gilbert. Practise it slow and it will become natural after a few days