I think character selection plays a huge role in choosing what method you want to use for jumps. For slower characters you may want to use X/Y button to maximize aerial control (jump with button, horizontal movement with control stick) since spacing is crucial. I personally use Y.
For spacies on very high level, you may want to utilize all 3 options. I personally use Y for normal aerials and wavedashes, X for multishines (best position for sliding thumb to B button), and up for out of shine aerials/up B (for Falco) or SHDL (for Fox). The reason I use up for shine aerials is that it has the least movement on the hands... which means greater control and speed.
Comparing the two options:
1. utilizing button jump:
left thumb: down
right thumb: B
right thumb: X/Y
right thumb: C-stick aerial or netural A
2. utilizing up jump:
left thumb: down
right thumb: B
left thumb: up
right thumb: C-stick aerial or neutral A (it actually may be quicker to use your palm for C-stick left input)
By utilizing the up jump you negate the movement from B to X/Y then back to aerial input. You instead get an extra controller stick input but I think it's a lot faster due to less thumb movement and lack of a button press.
As another tip, some people go from X/Y to Z for quick nairs. Instant nairs out of jump is crucial for some characters like Shiek. Doing a quick tap from X/Y to Z may make it easier to do this than going X/Y to A (due to the fact that you can partition the two movements between two fingers rather than shifting through two buttons with one thumb).
Regarding which character you might want to start using:
If you are laid back and want to enjoy the game: start with whatever character you like and feel comfortable with. I'm pretty sure a lot of Samus mains out there started because a hawt blond girl pummeling others in armor was a turn on for them. And the sex kick is good.
If you are a perfectionist, spacies/falcon are going to be quite frustrating. If you watch high end play on youtube you will see that APM and control of those characters are QUITE overwhelming for a new player. Complete control over those characters will take immense effort. I recommend playing a slower character and building confidence and knowledge of the game before switching to these chars.
If you just want to win matches, I recommend starting with the slower characters on the top and high tier list (Marth, Shiek, Puff, etc.). Build tech skills, match up knowledge, and spacing techniques and then, if you want to, move on to the more technical spacies.
I've been playing this game since the day it came out but only learned about ATs last year. So as another guy who started ATs late, I think my opinion would help. Also if you want to get better quick, you need to find certain types of players around you. Ideally, you want to play against players that are much better than you (mid-high competitive level) and players that are on the same level as you.