Ever since I switched to an Arcade Stick my 3rdS skills just disappeared.
Switching to stick is cause for some initial loss in ability, but the real reason is your switching to AE as your primary played game. You can't expect to retain 3S skills if you don't play it, especially if the other game has much higher input leniency, as is the case with AE. 3S is my main game, but still those long sessions with you in AE end up giving me some temporary issues when returning to 3S.
I use an 8-way gate myself and I much prefer it to the square. Even though I am quite able to use a square, I just feel I'm more consistent with the octo. Although I do get a lot of stick (pun INTENDED) from my mate, who maintains you should only use square. Just in case you ever play at an arcade or use someone else's stick.
When I was new to stick, I favored the octagonal gate, but after a few years, I can barely play on octagonal or circle. Everything but square feels unnatural to me now...