When it comes to crystal, the original intent and design was not for them to be interchangeable. Different ships had extremely different costs in metal and crystal, and so you'd have to balance which planets you took partly based on evening out your resource needs to what you were trying to do.
IE, a lot of the starships cost a lot of crystal, and so did bombers. So if you wanted to pursue a strategy heavy with them, you had to look for planets with lots of crystal on them. That was another consideration alongside the strategic importance of planets and the defensibility of the planets. It was a MAJOR consideration, come to think. And not just in the early game.
And there were often times where we'd be playing and dividing up who had what planets so that the metal and crystal resources could balance out the way we needed them to. Or gifting extractors as needed to even things out, either way.
Then at some point, the ability to convert metal and crystal back and forth between one another was added. I don't remember if this was in response to player request, but I think it was just something I decided to do. I liked the idea of a "market" like in Age of Empires, but in the end the market here did not function at all as interestingly or as effectively as the one in AOE.
So then we had a slippery slope. Conversion got automated in various ways, and then made completely automatic more recently. With these things, the difference between metal and crystal did indeed become pointless.
But even going back to just my first introduction of the manufactories... I feel like I can safely say that that was a mistake at this point. Bad design call, because it made the whole decision-making process of which planet to take a lot easier in a bad way. Certainly there are plenty of decisions going into what planets to take these days, there's no question. But I think that some of the defensive strategies and the ultra-low-AIP strategies are made a bit easier by not having to consider planets for their M+C ratios.
I think that, in the current design, removing crystal makes a lot of sense because it really is pointless.
HOWEVER, I also think that the original design is better. The way to get back to that is simple: entirely remove the ability to convert between the two. If you wind up with huge amounts of crystal and no metal, then oh well! Better shift what sorts of things you are building, etc. It's a lot more interesting in terms of you having to react to the terrain of the map, and adjust your build strategies accordingly. That's the positive side.
The negative side is that it causes a bit more micro. You have to watch your M+C more, and if you've lost some key extractors for a while then you wind up having to adjust build queues to compensate. So there is a lot more fiddling with build queues, relatively speaking. It's not horrible by any stretch, but it can get frustrating from time to time. I sought to dispel that lower-moderate frustration by introducing manufactories, and in so doing caused many more problems.
1. Since this is a good beta time period, there is freedom to experiment. For now, just remove the ability to convert metal and crystal. See how it feels. Some people will undoubtedly cry foul because it will cause play styles to need to be adjusted. But let's just get everyone to at least give it a chance and see what they think. It's hard to evaluate something like this on paper, and it's an easy thing to change (and change back, as needed), go giving it a try in beta makes a lot of sense to me.
2. If people really wind up hating it, then I suggest that crystal be dropped. And promoting the hacking stuff up to the interface there is probably then a good idea.