costs escalate way too much that way. Underground metro is around 600 crore/km while over ground (elevated) its less than 150 crore per km. Even when you factor in escalation due to delays in land acquisition, it makes sense to go for elevated line (and make nearly everyone suffer while waiting/giving compensation) than underground. This underground cost vs elevated-linked problems is what's jeopardising phase 2 of mumbai metro, which is sad when you consider how effective phase one has been.
Under sea is no good, it would end up being north south in direction, and for north south travel our very WR/CR is more than sufficient.