chargecooler isn't as affected by ambient temps as an intercooler. Chargecooler also can be fitted (generally) closer to the throttle body, reducing lag (less pressure drop/less piping). Also means you've the side effect of not obstructing the main radiator - leading to overall lower engine temps.
The downsides are the more complex system, plumbing, and additional points of possible failure.
Water absorbs heat 4x slower than air, so keeps the temps down longer (especially when used in a short sprint setup, drag racing etc). However, the flip side is of course it also releases it's heat 4x slower too.
Of course - one you've got a charge cooler setup, there's nothing stopping you trying to drop the water temps below ambient for those special moments - think ice cubes in the water, peltiers etc).
Then you'll be getting serious low intake temps.