I don't see either of them touching each others' scripts. Brocka rarely went into a multi-story, multi-character script like Manila By Night, dependent on shifts of tone and clashing scenes of horror, black comedy, and drama, some of it from late Fellini (maybe the one significant film Brocka did dealing with several storylines at once is Tinimbang Ka Ngunit Kulang). Bernal, on the other hand, wouldn't go for something as straightforwardly sentimental as Maynila, with its innocent probinsyano and soiled angel of love (Ligaya Paraiso--the name still makes me grin). He probably couldn't muster the conviction, and he'd turn it into a parody of some kind. Kind of interesting thought, that, however.
I'd prefer Maynila. Bernal's look for Manila hasn't aged well--it looks actually like a clean, fun city to party in (it's the characters and their relationships that have retained their unholy power). Maynila, on the other hand, with a genius cinematographer like Mike de Leon working on it, still defines the look of the city in our--and the world's--imagination.
That said--there's something about O'Hara's Manila movies--Condemned, Bulaklak sa City Jail, Bakit Bughaw ang Langit?, and above all, the fantastic Bagong Hari. I wouldn't say any of these movies replace Maynila, but they offer an alternative and I'd say more complex view of the city than Brocka's. Plus the action scenes in Bagong Hari, for one, go beyond anything Brocka has done.