to throw in my hat. i love the whacky asthetic of sr4 a lot more. and hope they continue to make the series even whackier
the ending for sr4 has made a world of possibilities for a possible sr5.
personally, since zinyak can indeed travel through time, i am thinking of a zin civil war.
where the zinyak of the past finds out about his defeat and rallies his then-followers (as well as forming an alliance of the saints previous villains, including dane vogul, the general, mr sunshine, julius little, phillipe loren, maero, junichi, and killbane, all ripped right before the protagonist would have fought them) into fighting the saints and the current timelines version of the zin. however, an otherworldy being sees the potential damage to the universe and pulls both factions into a city of its making ripped out of time. a prison for any and all time-traveling ner-do-ells. but the saints and zin, still hated enemies, continue their war.... while also trying to escape this limbo with the help of inmates who ALSO are trapped there.
the boss still has super powers, but he loses them at the start. he slowly would get them back as the game progresses, along with new ones.
and although the previous villains ARE indeed working under the past zinyak, they all form their own gangs and are warring amongst themselves, as well as the saints. yeah. the ronin, the masako, the morningstars, the luchadores, the sons of samedi, danes ultor, and the brotherhood are all back and badder than ever. and they hate each other. and they hate you. the time-rift explodes into a massive gang war. and at the center of it all, the angels (this version of the law enforcement) are trying to stop everyone from destroying the universe, and actually have super powers. in fact, by the end, all the gangs are super-powered. and its an all-out war. the civilians (yeah. there are civilians. why wouldnt there be?) are all simply people that are trapped in said limbo.
the final battle would end with the boss bascially beomming god. and with his rule, he ensures one rule: chaos above all.