During syndicate wars, make the win/loss relevant. Perhaps bonus points for the winning team?
I'd rather auto collect be a button or something. Accidently moving your device would collect everything. What if you wanted to just collect some of your buildings and leave others to sync things up. They could make it an option in the settings menu: turn shake to collect on or off.
They should give us an option to upgrade two buildings at once. Especially two IDENTICAL buildings. We should be able to upgrade them simultaneously, with it only counting as ONE upgrade, if an expansion is also purchased.