Well, the towns from GS not showing up in TLA were due to the fact that you don't have access to those areas from the original GS (I'm aware of the boat glitch; I'm speaking legtimately).
Between TLA and GS, we had access to all of Weyard, and a lot of the peoples (Sana comes immediately to mind) aren't mentioned or referenced to exist (I realize they may not have been thought up in development yet). In this new game, it seems like they went overboard with the ancient civilizations and how all of a sudden everyone in every town is a history buff, but rarely even mentions the Angara towns that existed (I haven't heard any mentions of Altin, Xian or LUNPA so far) in the previous games.
I find this game most fun and interesting when they're referencing back to things we've actually seen or heard of before. Frankly, there are just too many ancient cultures that suddenly became common knowledge since the Golden Sun event just 30 year ago. Don't get me wrong, I'm willing to believe that all the new towns/ruins jutted up out from underground and that the old towns were destroyed (they twice directly state that two of the towns were destroyed via the GS event).
AND I HATE RYU KOU.
But I do love the new summon directly lifted from the original North American Golden Sun
.And HOLY CRAP YES the Saturos battle theme is back!