Twice now the plugin has become nonresponsive, forcing me to kill the process, and both times I lost part of my progress (even though I saved several times), putting me back to right after getting the "mine 10 rocks" assignment in the tutorial. It's a little annoying.
What the heck is up with the new boss? Everything before was stuff I could handle somehow without spending too much DP, but suddenly there's one with 2 Jinzos, some big explosion and shared fate all monsters, and 2 of that ugly thing that gains 4000 Power and becomes Immune each turn because he has a 15-monster deck. It's like they decided to put up a paywall.
I have lost count of how many times I've died because the game stopped responding to my actions when I was in the most trouble - losing 10 seconds because the game makes you spend 5 seconds at empty space after taking down 1 enemy, and then overshoot when trying to change aim to the other, ruins your chances at survival.
There are far too many issues to make this a decent game - if you die while moving, in a lot of levels you'll die twice because your movement will carry over into your next life, killing you; if you're pressed against a wall and fall straight down, you'll die from 'touching' a spike adjacent to your square, and on level 30, there's a nasty spot where being pressed against a wall prevents you from double-jumping.
It's annoying that you can't do anything while the game is paused (even change pages in the manual) - I'd much rather be able to change my employees' hours, promote them, and build and upgrade booths while the game is paused, rather than have time tick away slowly.
You should be able to perform certain actions while the game is paused, like promoting personnel - trying to click on them while they're moving among a crowd of customers is annoying.
Only having a 100% line isn't very useful when trying to hit at 110%, or when you deliberately want to hit at 90% to approach more slowly on a chip shot.
It's a little grating to get to 398/400 achievements only to find out a glitch is preventing you from claiming an earned achievement (in my case, loose change - testing room).
Weird... I spent about 5500 days building up a cash reserve of over 10 million before actually going ahead and beating the game on Hard, then when I started a new game on Easy, I got the 90 days, 75 days and 60 days achievements.
The entire point of games like these is to cautiously take advantage of flaws in the paths the guards take, not run around and hope you get lucky. When you randomize their movement this much, you take away the biggest aspect that makes the game fun.
As someone who likes to mute games and listen to Winamp instead, I'm annoyed by the music's tendency to start again whenever I go to the level select screen or the upgrade shop. Please fix this.
 "Astrox"){kind=icon}
 "Yu-Gi-Oh! BAM"){kind=icon}
 "The Last Stand"){kind=icon}
 "Road of the Dead 2"){kind=icon}
 "Shotgun vs Zombies"){kind=icon}
 "Give Up"){kind=icon}
 "Fear Less!"){kind=icon}
 "Cleansing"){kind=icon}
 "The Great Siege"){kind=icon}
 "Shop Empire 2"){kind=icon}
 "Turbo Golf"){kind=icon}
 "Achievement Unlocked 3"){kind=icon}
 "Zombies, Inc."){kind=icon}
 "Ultimate Assassin 3"){kind=icon}
 "Liferaft: Zero"){kind=icon}
 "Heir"){kind=icon}
 "Kids Vs. Ice Cream"){kind=icon}
 "GoonDoo"){kind=icon}