The point is to make everything untargetable except by mass effects. The invisibility is just a cool special effect. You could basically think of cloak as reading "effects that target individual cards may not be cast on your cards, except this one." At least as far as the AI goes. In PVP, where you can actually psyche out other players by not showing them what you're casting what spells on, etc, it might be different -- but since they get to see the cards you're casting in the first place, it's actually not really all that. Things that can be cool, though: Mutation, Fate Egg, Nymph's Tears if you have multiple Pillars out, etc.
Interestingly, the AI plays very intelligently w/Cloak, I'm impressed at it's ability to seemingly 'figure out' what's happening on your side of the board. For example, I was chaining Cloaks, and it waited until it had seen me cast 3 creatures before casting RoF and breaking the Cloak. Very cool.