I feel obligated to defend Puyo a bit here - I'll level with this and say the gap has significantly closed over the last few years, and Sega tends to treat Yakuza with a bit more esteem, but I feel like that has to do with Yakuza projects generally being higher budget, AAA level affairs. That's how I'm reading this report, where Sonic / Yakuza / Persona are Sega's big three AAA franchises while Puyo Puyo - despite reportedly being their strongest brand in Japan and last I checked still being Sega's second best selling IP - are just not eyecatching blockbuster games as much as it is a reliable, consistent cornerstone of the company.
I think if you went for Puyo, it'd be more under the guise of a significant legacy series and playing hard into its arcade roots. Less to keep things contemporary, moreso to respect the history. Smash is no stranger to taking this angle instead and frankly, it would be welcome among Sega's current lineup.
I'm unsure what would take precedent though, I think there are strong cases from either side. In a perfect scenario I'd like both Arle and Kiryu / Ichiban in the game. Would be inclined to say Puyo may be more likely for a base roster pick, and Yakuza would be a killer DLC pick akin to Joker... which, suffice to say, the confidence in Persona to the extent of promising yearly content does bode well for Joker's return or some new Persona representation in the future.