Interesting, I can see why D3s would want to go to any walk-off stages.
Thing is though all the ones Gates mentioned are from transition stages, meaning they aren't permanent. So while it's not something to like ban or lose that one match out of the set, you still need to concern yourself with that fact.
If I had to pick a stage out of all of them to ban, I would go with Delfino Plaza, since that stage has more walk-offs that are harder to avoid; At least Castle Siege's second stage that has the walk-off can be avoidable by just camping the statue platforms, or the non-destructible. I would assume stalling, whether you're in the lead or not, is not worth risking losing that one stock, because Sonic is CGable, and at perfect play you can expect that Spring won't get you out if they are frame-perfect with this.
P.S. Delino Plaza has clear walk-offs, meaning it will be much harder for you to run away in that time, not to mention I already know the stage has at least two walk-offs.
Okay, now that we're talking counterpick stages to go to, let's find out where exactly D3 excels and lacks so that you can take advantage of it:
D3 has the worst aerial speed in the game, meaning stages like Rainbow Cruise where you have to do some jumping are recommended... whether I personally would CP D3 here is something different, but at least you know that he's not just too slow, but
THE slowest in the air.
Without any edgeguarding tactics, D3 has a pretty decent recovery, him being very heavy with 5 jumps, and another jump that takes him quite high and has Super Armor on ascension. Sounds pretty good right? Wrong. At least not against Sonic anyway would D3 want to be in this kind of position. Being heavy is a problem when he's not outright killed because it will counteract his chances of getting back onstage, add that he is very big and that he has less to work with in the air (confirmation please? I know there's 5 aerials (though Nair and Bair would seem useless when you're trying to get back on stage... unless Sonic somehow messes up and ends up behind D3 lolwut?) and an airdodge). Sonic also being quite the edgegaurder... well I guess I've already emphasized how important is that you need to have D3 ofstage.
D3 can chaingrab Sonic, don't let anybody who isn't frame-perfect confuse you. It's not so bad when Sonic has a decent recovery but considering that everytime you get grabbed you will have constant damage being tacked on you, you don't want a really flat stage like FD (though it's not the worst stage you could be on, probably just the worst neutral maybe), you'll want a stage that's rather small or changing in some what so that it isn't just... blecktch.
Anyway now you also have to factor that not only can D3 have the same damage output as Sonic, but you also need to consider that you can be killed much earlier than he can. I don't know how smaller/bigger stages work with this equation, but I find that stages that have more open space offstage and/or farther blastzones are better for you. At least with those you'll be able to live much longer and have a better chance of getting some offstage/gimp kills, whereas D3 will moreorless have the same work to do, if not more.
No walls. Stages with permanent walls are almost as bad as walk-offs. The only difference is you just have to be baited to that one part with the wall and it's 1-stock good bye.
With all this said, what would I say make the best Counterpicks? The best stages I feel that meet this criteria are Frigate Orpheon or Pirate Ship. Frigate is a very small stage with it's blastzones quite far away, not to mention the small stage works better if your favor than it does for him. Pirate Ship, although on the opposite of the spectrum, is alright. The stage may be very big for you to get grabbed, but hey, more space to work with, and the hazards certainly make it risky for D3 to try and continue something onward. He doesn't have a spike, so you'd be fine with or in the water, though you won't ge getting any gimps, you shouldn't be dying anytime soon yourself
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For neutral,s I'm not sure, you'd probably want to go to Yoshi's Island. It has big blastzones, it more or less small, not entirely flat, and iSDR is here.