Wow, Lino vs. Ishma? That's several articles, maybe a book's worth of comparisons.
Off the top of my head, and please don't hold me to these statements, Bernal was the subtler, more understated storyteller. Yes, he was more comfortable with the middle to upper classes, mainly in the city, but he could do the occasional great film set amongst the poor (Himala, Nunal sa Tubig), he was more versatile (he did horror (Frigidyer), action, even a Superman movie). He could ring down all kinds of emotional nuances, and he was a great comic director, and you know what they say about comedy vs. tragedy.
In comparison, Brocka had a limited range, was only subtle up to a point, and I don't think he's ever made a quiet movie in his career (the closest could be Ina Ka ng Anak Mo--significantly, set in the middle classes). But his best works represent the very heart of the Filipino, I'd say. Bernal was the sophisticated internationalist, Brocka the homegrown storyteller.
That said...the two of them were worthless on action movies and noirish action, the, uh, 'proving ground' of truly visual filmmakers. Know who's better? Tikoy Aguiluz, Celso Ad. Castillo, Mario O'Hara.