I'd suggest that Mercenaries shouldn't require the corresponding MkII ships to be unlocked in order to build them. The mercenaries are so expensive that this restriction isn't necessary and it's thematically inconsistent anyway. If the player wants to spend a huge amount of resources on mercenary ships at the beginning of the game, let them, it'll put them at a disadvantage.
Good point. Changed for the next version.
The mercenary system could also be developed further, for example, I think it should have a completely different model to the standard space docks. Purchased ships should appear instantly, but there should only be so many available for purchase at any time. Recruitable ships could vary by planet, and precisely what's available could rotate every so often. Recruiting a passing band of Zinth fighters could be cool. 
That's really a different kind of mercenaries model than what I have in mind. It's something similar to what I've seen in other games, but I was never as fond of those because they require so much micromanagement as well as periodic checking. Maybe "mercenaries" is a bad word to use for the concept I'm trying to advance here, but it was the best thing I could think of and I think it is fitting in general. I basically just want to have ships including a few niche classes that are nowhere else, all of which are expensive but uncapped, and which are as easy to build and manage as everything else that is queue-based.
Recruiting passing Zinth starships, or whatever, would probably instead be handled via trade with the Zinth in a future expansion. I think that's basically the concept you are going for, where you spend the resources one time and then they appear instantly, and in the case of the Zinth trading it will also include a lot of specialized alien ships that you can't get any other way. That's really where I see a concept like that coming into play, but it's for an expansion focused on the Zinth.
As Fiskbit pointed out in another thread, I agree with him that the addition of mercenaries is not a solution to the excess resource problem. It's just alleviated it somewhat, the current situation is "I've built everything, well, nothing better to do than buy some mercenaries", while previously it was the considerably more interesting, "I can't afford everything, where would my resources be best used?". Essentially, having fewer resources will create more interesting decisions.
Okay, well, this is true enough. I'll respond more in the other thread, but my hope is basically that making resources finite per planet will help. The main problem is that I don't want people to have too much downtime while waiting for stuff to rebuild, or waiting for resources. And with lower resource rates in the new flow-based economy, it is just far too easy to tank your economy -- the old model could only support
two simultaneous space docks, with no engineers assisting them. Anything more and your economy would periodically tank.
I'm not saying it is balanced perfectly now, but basically I generally like the inflow numbers compared to the outflow numbers at present, and I'd like to balance this in other ways. But perhaps I'll change it so that harvesters only generate +10 instead of +12, and see what that change does.
