The game is impossible to play at high resolutions due to the tiny size of the Secrets and the darkness. Ramping up your monitor's brightness washes out some of entrances to the tunnels.
Make the Visitor's actions more consistent (why not invade the dog like you had the cat), make interaction more consistent (click on the Visitor to use it's abilities and click on objects to use them), and the sudden switch in perspective for the final scene was jarring and detracts from the game.
While I appreciate the addition of seeing balloon hit points left, the problem with it is that you have mouse over the balloon to see it. That seems a little annoying in a game based on leading your shots, and becomes aggravating coupled with the fact that un-clicking the mouse button sets your turret to reload, crippling your ability to react.
You gain time when you clear a square, but also score points. At lower levels, don't solve the game but instead continue to clear squares. It's a slow method of racking up points, but works -- high score goes to whomever is willing to spend the most time at it.
Potential spoilers! (Haven't played the sequel, perhaps it answers these questions?)
Two storyline inconsistencies. One, why would you give your gun to someone, just because Rhodes says he knows the guy? Normally that means he could just go up and talk to the guy.
Second, why would you refuse to make the speech if you don't believe you're Jason Greene? Threatening to kill you even after you made the speech makes no sense either. Rhodes should be satisfied that the law will punish you once the truth came to light.
 "Tower Defense: Elsopapeador"){kind=icon}
 "Airport Tower Defense"){kind=icon}
 "Recordshop Tycoon"){kind=icon}
 "Submachine 2: the lighthouse"){kind=icon}
 "The Visitor"){kind=icon}
 "Balloon Invasion"){kind=icon}
 "Blocky"){kind=icon}
 "Reverb Part 1"){kind=icon}