Yeah, you make a point, I suppose: I just wish there was a way to let Sakurai know we still want Isaac as a character and not an Assist Trophy.
There is no way, because its blatantly obvious. Sakurai knows we want Isaac as a character. He's an Assist Trophy for any number of reasons, but not because he doesn't think fans want Isaac as a character. Many Assists are characters Sakurai knows fans want to be playable. That's the reason they're Assists to begin with. So they can play a big role despite not being playable.
So, why is Isaac an Assist Trophy? Again, we can't possibly know until Sakurai asks, but there's several options.
1.) Sakurai doesn't think Isaac is feasible as a playable character. This is extremely doubtful. He clearly knows how unique Isaac would be.
2.) Sakurai thinks Isaac is too niche. Well, in terms of sales, Isaac is around the same level as Pit, Shulk and Olimar. I kinda doubt this is the case, tbh.
3.) Isaac wasn't as massively requested as we all thought. While this is an interesting thought, I kinda doubt that's the case. If he wasn't that requested, I kinda get the feeling he wouldn't have gotten an Assist Trophy at all and maybe got a Mii costume instead. Other than Gray Fox, who is obvious why he got cut and came back now, Isaac is the only other cut AT to come back.
4.) Isaac was massively requested, but not enough to get him to be considered over the current characters we have. This is definitely more in the plausible range, and is probably the most likely scenario. They mostly focused on veterans, which limited additions of new characters. They split the new characters between massive fan requests and recent characters.
5.) Isaac was massively requested, and Sakurai really wanted to include him, but Isaac was a bit too complex compared to other characters and with all veterans back, he didn't think there'd be enough time for Isaac to be added into the base roster. Maybe he wasn't as big as Ridley/K. Rool, so he just barely got cut as a playable character.
6.) Isaac's Assist Trophy is only a stopgap for playable DLC so that Golden Sun plays a role in the base roster beyond merely Mii Fighter costume or Spirit. Isaac is one of the 5 DLC characters.
I really really want to try out Golden Sun. Is it on the Wii U? Even so, I might just get a GBA Cartridge instead, either to have a more authentic experience or in case the Wii U version blows hard.
I kinda wish that Golden Sun, or the Lost Age, was on the 3DS Ambassador Program. (Let's say it replaced Mario Kart: Super Circuit, the worst game on there IMO or at least the most expendable). Then the series would probably thrive on to this day, as opposed to being left in the dust.
Golden Sun and Lost Age are both on Wii U. Dark Dawn is not, but if you purchase the cartridge you can still play it on 3DS.