It might not be franchises that you care about, Sega still has several good Japanese franchises under their belt (doing the distinction cause remember Sega West has their own franchises separate from JP; Football Manager, Total War, etc) ones.
Yakuza, Puyo Puyo, Valkyria Chronicles, Project Diva and the recently released Sakura Wars, etc. Not to mention they now own Atlus which means they now have Persona, Shin Megami Tensei, Catherine, etc.
Now don't take this as an official explanation / reason but.... Sega doesn't really consider the Global market when developing titles half of the time, they mostly develop games with the Japanese market in mind and then from there simply localize those. What Japanese fans are nostalgic about with Sega is really different; remember that while majority of fans consider the Megadrive (Genesis in the US) era to be the most important for Sega.... in japan the Megadrive was a failure, lagging behind the NES, SNES and PC-Engine. Sega's decision to suddenly abandon the Megadrive for the Saturn didn't make sense in the West... but it made sense in Japan; Sega really wanted to move on from the Megadrive and have nothing to do with it.
For this reason, a lot of so called "Sega franchises" from th Megadrive era are mostly in a state of limbo are simply being given to outside publishers and developers to deal with it (like is the case with Streets of Rage 4). For Sega, the Saturn and Dreamcast era were at their peak and what they are most remembered for... in Japan.
Of course i'm well aware that my theory doesn't cover say.... why Sega didn't make the Panzer Dragoon Remake themselves, why Panzer Dragoon, Space Channel 5 and NiGHTS into Dreams lack collabs (ironically the last two in this list did have collabs in PSO1 though). Like someone else commented here say... collabs don't (usually) happen for the sake of collabs; the franchises depicted in the Sega Legacy Pack (7th Dragon aside) were ones which had a large fan following in the West (Yakuza, Valkyria Chronicles, Puyo Puyo, etc) and were conveniently available around the time of the game's PC launch. The Miku and current Sakura Wars games are coinciding with the fact that both games were recently released in the West; Hatsune Miku: Project DIVA Megamix and Sakura Wars (Shin Sakura Wars this year).
As an additional fun fact... in the Japanese version at least, the screens in the lobby also display ads for many of these upcoming Sega games too.