I actually thought Manning's arm looked stronger than last year. It's a brand new system and he didn't get that many preseason snaps because the new line wasn't trustworthy yet (and as you can see he took 4 sacks yesterday).
His timing was way off, but I believe it will get better. The running game didn't do crap for the first 2.5 quarters and they are going to have to rely on it. The passing part of the playbook is set up by the run game in this system. It's going to look more like the Edgerriin James era Colts.