Apparently OP and most of the people in this thread just skip the dialogues and complain about bad writing.

Graha have memories of his ancestors because the last Allagan princess saw the impending fall of her empire and implant her will and memories into his forebearer.

Secondly, he chose to seal off the tower because the NOAH and Cid's team aren't at the stage where they can utilize the tower and the Allagan tech for the good of the realm yet. Why do you think when they said their farewell, Biggs was clamoring about how they will get to surpass the Allagan and come back to wake Graha up?

Lazy readers.