I just completed the game and wanted to play again with another way of finishing the game, so i can get different endings. But when i play it again or replaying a mission, the power and ability that i have had after i completed the game is gone. I have to start all over again with no power and ability. Is it really like that? so i cant have full power and ability to play it again after i beat the game?

Nop, it's like that. The 'replay mission" feature actually load up the equivalent "mission : XXX" save. With the progress you did last time you played the campaign.

So if your latest playthrough was, say, a full low chaos - no powers run, every mission available to replay will feature a low chaos setting with no runes spent on powers. You will also retain the charms you found so far. If you start a new game and go on a killing spree with High Chaos setting, though, you will find out that your low-chaos/no power replays are getting replaced.

it's kind of lame, in a way, yeah. There should be a mission parameters customization or something. Like choosing between low and high chaos, which upgrades you have, what powers, etc.

Not sure... I kind of like it the way it is. If you want different powers, do a different playthrough.