How damaging (if at all) would the Mamluk system of government be to their prospects of long-term survival? Their half-hereditary, half-acclamation-of-troops system of inheritance made periodic internal rebellions almost inevitable, as well as exposing numerous political cleavages that a potential invader could exploit for advantage. Reliance on Mamluk popularity might also have discouraged Sultans from pursuing the sort of comprehensive reforms needed to compete with other regional powers. I know the Mamluks historically managed to maintain their state for about 2 centuries; I'm just not sure how they did it and whether their 'survival methods' would carry on into the early modern period.
In any case, should the Mamluks survive past the 1500s I suppose their key concern would be to maintain the viability of the India-Egypt-Venice trade route in the face of aggressive Portuguese expansion. A divided Middle East might also have seen the Portuguese take greater risks than they already did, especially regarding raids in the Red Sea or even for Mecca itself...