MASSIVE WALL OF GREEN TEXT RAWR!!!!
Here's some funny things to note.
1) Some samus' will actually ban Kirby 64 vs you, because they dont want you living for a long time (this actually happens to me ALOT vs samus)
2) Corneria is actually a terrible stage to take Samus to. I dont know all of the details; but i know they can fin combo better than you can.
3) Pokemon Stadium is not that bad unless the samus is obviously missle heavy, and even then it's not so bad. Pills > Missles. And the funny thing about the PC Missle spam trick is you only have to deal with 1 row of missles, it just seems so bad because all you hear is (BOOM BOOM BOOM BOOM BOOM BOOM)
4) If you're afraid to take samus to PS for misslespam, you should be afraid to take them to YS for missle spam. That platforms on both stages are the same height.
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Now, with all that being said.
Yoshi's Story isnt a bad stage to take Samus. Not great mind you, but it's probably your best choice of all neutral stages.
Final D is ok, but your pill game has to be onpoint to combat missles, and you have to space yourself very will because samus straight up TILTS DOC TO DEATH.
A good counterpick, however, is Kongo Jungle 64. Why? She cant grapple; and it's kind of hard for Samus to sweetspot the edge. The big downside of using this stage is that Samus usually has the top platforms as a recovery option and you usually dont.
Rainbow Cruise and Pokefloats are ok, too; but it's kind of hit-or-miss with those.
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And just because somebody is going to say this. Battlefield doesnt hurt a (Good) samus's recovery at all. It changes it, yes; but doesnt hurt it.