I wouldn't upgrade the wheels. Stock wheels are decent if no name.
A carbon fork is a nice upgrade to an alloy bike. If you can't afford one, a cromoly one will do. They have good dampening characteristics.
Like I said, putting on a cruiser bar is the ticket to a more comfortable bike. You sit bolt upright and take the strain off your hands, wrists, arms and back. You can see around you and you can breathe more easily.
I think your Giant Escape makes for a decent city bike. Later, you can add fenders and a rear rack if you want to go commuting.