I would prefer bans to remain consistent regardless of 2/3 or 3/5. Reason for this is two-fold:
1. Different tournament sizes or different regions can have variable bracket qualifications for how deep you need to be in bracket to encounter a 3/5 set. A small local that's pressed for time may only do 3/5 sets for the trio of Finals, while a national could do every top 16+ match as a 3/5. This is an inherently inconsistent split that's bound to come up, and it's probably not good for rule formats to split + split without total consistency.
2. People want to play basically the same game as everyone else. Making the game count longer is not a drastic shift (DSR affects MU's as the set count increases but that's to be expected), but changing ban power / stage legality / other things means that those players are legit playing something quite different than what you were playing. Take Melee 3/5: Jiggs always gets Dreamland, Marth always gets FD, etc. That's a pretty different experience than the average person in bracket playing those characters.
Having the game split into "Oh in x normal format, these 1-2 stages will never survive banning, but in y format once you get to top 16, you can almost always play somewhere on those stages" is not something I see as desirable. Keep bans the same, change DSR or add onto the stage list. My gut says add 1 more stage to make 10, and keep 2 ban consistent regardless of 2/3 or 3/5. Norfair, Lylat, or Yoshi Brawl are probably the most likely candidates. Norfair may be the least controversial choice?
If none of those are suitable to add-on, consider reducing stage ban to 1? In all honesty, 2 ban power in 9 stages is pretty hefty: almost half of stages removed after 4 total bans. 2 ban in 10 stages is a bit less hefty, and it leaves 6 stages minimum to play out 5 games without DSR changes or any other rule tweaks to accommodate 2 ban power.
I don't have a lot against the stages in Nebraska format: don't have much of an opinion about Bowser stage but the rest seems fine. I think bans changing because of 3/5 sets is the issue to solve.
TL:DR
In Nebraska list, assuming 9 stages and 3/5 sets dropping down to 1 ban, please instead keep ban count same for 2/3 and 3/5 sets. Change DSR rules OR reduce all ban counts to 1 OR add stage/s instead