When I saw the Assist Trophy today on pic of the day I first thought that it was an Assist Trophy inspired of a summon from Golden Sun due to the size, but then I quickly realized that its design didn't match the Golden Sun universe very well, so I did researches about him and without surprise it wasn't a Golden Sun summon. For half of a second I though it was teasing for Golden Sun content, meaning the possibility for Isaac to be on the playable roster, so much disappointment
Personally I don't think that the dormant state of the series is a very strong argument. The last Punch-Out!! game was released
one year before the last Golden Sun game, still post-Brawl, and despite this Little Mac was eventually promoted from an Assist Trophy to a playable character, five years later that this last Punch-Out!! game. Also yes, Dark Dawn was kinda disappointing compared to the GBA games (I only played the first Golden Sun so I can't compare myself, I'm just reporting what I read), but Skyward Sword and Other M got a lot of negative criticism compared to previous Zelda and Metroid games, and they're still represented a lot in SSB4, though I admit that it's maybe because both are already well established series in SSB.
Actually I think that one of the biggest problem Isaac is facing, and maybe the reason why he ended in Brawl as just an Assist Trophy, is because of the "uniqueness" Sakurai wants for the characters in SSB. "What?! Isaac has so much potential to be unique!" I expect from you, but there is a problem - uniqueness isn't based
only on the moveset potential, and we already have these guys in SSB:
The entire Mother series has been released on Game Boy Advance, hurting the chances of Golden Sun representation due of the similar game genre (RPG) and power used by characters (a psychic energy). At the same time Isaac looks nothing like Ness or Lucas (well, asides from blonde hair colour shared with Lucas) and the Mother series's relation to the GBA isn't as strong as Golden Sun's due to the fact that Mother 1 + 2 is a remake of two games originally released for the Famicon and the Super Nintendo respectively.
I feel that getting three RPG heroes with psychic powers from two franchises would maybe be overkill, though obviously I don't deny that Isaac would have no trouble to differentiate himself from Ness and Lucas as a fighter in SSB4. I'd like to know your feels about this case, especially from someone who played games from both Mother and Golden Sun franchises. GS proven to be an active series after Brawl thanks to a new game and the release of both of its original games on the Virtual Console (though we're still waiting for The Lost Age outside of Japan), and with the high demand from fans, I hope that Sakurai will look farther than "We already have psychic RPG heroes we don't need another one from another series" for this new Smash instalment!