I don't main Samus, but I do have some tips to deal with disadvantage as Bowser probably has just as bad of a disadvantage state.
When you're getting combo'd you can DI out and spam either airdodge or your best combo breaker move if you have one (for Bowser its side b, not sure if Samus has one though. I guess Screw Attack but don't do it unless you're sure it'll hit.)
I actually have a few tips for recovering as my friend is a Samus main and I've had to punish his recovery many times.
If you recover with tether, flick the left stick as soon as the tether hits the ledge so you get to it faster. Tether isn't an unpunishable thing though because if they know you're going to use it, they can run off and use something like Bowser fair.
When using down b bombs to recover try to drift in and out as you make your way towards the ledge. This way they feel unsure about going for a spike or not. You also want to be smart about when you grab ledge and how, because while it does do damage to those near the ledge there isn't anything stopping them from 2-framing with a spike.
All in all for recovering try to use as many options as you can in a single match to mix it up so you become difficult to edgeguard. For example, you can tether, but instead of flicking the left stick to the ledge, flick it down to cancel it and then recover with bombs and/or Screw Attack.
When you're landing, I don't really have much to say but you should definitely use your incredible air drift and down b to your advantage. Again make sure you don't overuse one option, this is something I've had to learn the hard way by having my Bowser's dair punished time and time again.
And finally, when they rush in, try and realize what option they're rushing in with. Like maybe this Roy really likes to dashgrab, or this Ness does a lot of spaced bairs. Once you learn their preference read it before hand and do whatever seems like the best option for your character.
I hope this helps with the disadvantage thing.
