I grew up playing 64 and not Melee...
Not everyone was fortunate enough to own Melee, let alone use the debug. I only have Marth as my Melee main to represent my secondary in PM (but I main him in Melee whenever I get the chance to play with my friend, however casual)
Debug can be useful in finding different techniques to recovering. I'm sure people will be finding frame perfect techs in the near future of 3.5 albeit they might be too difficult to perform consistently.
As for the blatant options where they presently stand, mix it up. Just be unpredictable when recovering. I like to always have at least two different options available to me in any situation. It's a good rule of thumb to never do anything more than twice too. For example, if you catch your opponent on the ledge with a f-air when you're recovering and then you do it a second time, mix it up by fastfalling then double jump into a wall jump or something. Alternatively, you could up-b early. Even if you have sub-optimal options, choosing them at the opportune time can prove to be equally useful.
If Samus starts to perform really poorly in the near future, PMDT will hopefully solve any issues. It isn't apparent to me that anything is wrong with her but I might be wrong. Yes, I can wholeheartedly admit that I'm not always correct. I'll just tackle any of my character's obstacles, come what may.
I'm just going to go play some Smash now, 64 or PM.