The design choices were wrong. Go read a book on UI design or spend some time working with end users interested in a happy, productive experience and you'll find that NONE of them want excessive popups or mouse clicks. None. Go find someone who works on CAD and ask them what their thoughts would be on introducing a few hundred clicks into their work day. They would throw you out of their office.
Introducing things that make people wait isn't suspense. It's just another annoyance. Popups and mouse clicks detract from a game. Name a popular game that's filled with so many pop ups. Seriously.
Your reliance on mods is great and all, but to use your game this is a CASUAL game. It wasn't easy for me with some programming experience to figure out how to make mods work on a mac. The better question is WHAT PERCENTAGE OF CASUAL GAMERS KNOW WHAT A MOD IS OR CAN FIGURE OUT HOW THEY WORK? Mods are great for the hardcore community. That's just a small percentage of your user base.
The game is broken because of these choices. While people here are tripping over themselves to defend it, it's a casual game and most of the users wouldn't participate in forums like this.
To the other folks with the troll comments, please grow up. Nothing I'm saying here is not factual or not based on anyone not playing the game. I spend a lot of time during my highly paid work week getting feedback from customers. We'd be laying off people if we sold products with this many UI issues.
As to the Tweak mod comment, you might want to look at the other thread I made here where more than one person was pointing out that it was broken.