This has original gameplay, being able to order around swarms of little ships is awesome, usually in flash games you order at most 15 units around and they just walk into a square next to an enemy and inflict 5 hp damage or something which is boring. I think you should make some more games like this and look at some other popular games on kongregate to learn how to make a user friendly layout and easier controls.
1: Allow more space to build.
2: Enemy doesn't attack before bar finishes, at least in the first 2 levels.
3: A way to deselect units.
4: Units follow a team leader so they don't attack one at a time.
5: Restart button.
6: Instant menu selections, no waiting for the screen to fade in and out.
There seems to be a problem with some buildings not transfering their products to the warehouse/town center but otherwise a very good game. I get gold smelters and blacksmiths with 100s of coins/tools in them. I think you should tweak the game a little so that anything produced is immediately in the marketplace or something.
You ruined the game with the "3 strikes and you're out" rule, so I make one tiny mistake when starting off then I have to do 10 levels again just so I can earn the same amount of money. Lame, I can't play this.
You need to make it clear that this game is based on transistors and stuff, that way people won't get so intimidated by the tutorial. That said, the tutorial isn't that great either, you should just have a bunch of diagrams instead.
Awesome game but there is a glitch, sometimes when I use shift and select to place multiple items I can't unselect the item, I've tried clicking select tool and everything but it won't work.
I've just started playing and I just attempted to join 10 multiplayer games and none have them have started, either the game is full even though it says it isn't on the main screen, or the host is idle. I also have difficulty finding a game that isn't full, usually all the games listed are 6/6 4/4 etc...
This is a good game and it should be interesting to a lot of people who use computers every day but don't have the faintest clue how they work, but you really need to playtest it and tweak it to make it more user friendly, that isn't to say you haven't achieved a lot in this department already, there are already a lot of suggestions here, my suggestion is that you make it so you can switch signal gates and off whenever you want so that you can quickly see all the wires and silicons are connected to it and how they interact, so you don't have to go through a verification test over and over when checking things.