The problem is 5 minutes CD for mining, and CDs for other gathering, right? Well, I have some ideas.
Either adding a way of reducing/removing CD - like when you mine, and get 5 minutes CD, you can do some minigame or something, I don't really know what, and it will take you, say, 30 seconds, and will remove the 5 minute CD. So you: mine, do something for 30 seconds, repeat. Or you could still wait those 5 minutes if you want to watch Youtube..
Now, every 5 minutes equals 5 iron ore / minerals, right? Well, if you could get more per 5 minutes, you spend less time overall, which also means less waits, therefore solving (partially) the issue.
This could be either by increasing the amount of resources gathered, maybe higher repair/science skill, more stuff.
Or, for mining and some others, you could get slaves, give them sledgehammers, go to some area with ore, and make the slaves mine too. If you would have, say, 4 slaves, and you would mine too, that's five times as much stuff. To me, that seems alot. Also, if you don't want to be slaver, you could maybe hire some miner mercs or something like that.
I've been thinking about it for a while, and I don't see why (parts of) it wouldn't work...