Since we're on the subject, I think Durantium and Promethium should be fixed too. For these, it's the opposite problem. There's entirely too much of these resources on the map. It's easy to gather way more of these resources than one can actually use. I've had games where on the trade screen the AI had thousands of these resources.
In the game I'm currently playing, I have resources set to "rare." That does seem to the case for antimatter and especially elerium, but durantium and promethium are still extremely common. I'm playing with several large sectors, and I've managed to take over three smaller ones so far. I'm 11 hours in, or about half-way through the game. I usually have between 0 and 10 elerium and antimatter, and I have to carefully manage my use of these resources. I can't really build any of the elerium upgrades for starbases because that resource is just so scarce. For antimatter, I have enough to get by, but not enough for every ship to have Harpoon missiles. (My military is split about 1/3 Harpoon missiles, 2/3 Enhanced Railguns.) I have a lot more thulium; I use a lot more of it, and I usually have about 20-30 in reserve. With durantium and promethium, even when I'm actively trying to use them up, I still have too much. (I have a lot of economic modules for starbases, I build promethium drives for my big ships, and I use frequently use promethium to fund research.) Still my durantium reserves have stayed over 50, and I have over 100 promethium now.
I share my experience from this game because it seems to be approximately the same for every civ in my game. We all have an extreme scarcity of elerium and an extreme abundance of promethium and durantium. This is a problem because it shuts down trade completely. No one wants to give away elerium, but nobody wants to take these other resources that are as abundant as dirt.
Early game there seems to be quite a bit of use for it, but by mid-game it seems like there could be some more serious sinks for the stuff. For something that is the "backbone of any strong navy" (per GC3) it sure doesn't seem like you need much of it. Maybe if you could sink some into every hull type to +hp, this would make sense for a resource in the amount that I tend to accumulate it.
Also there seems to be generally more available than can be used...
In my experience this is rare, although I haven't played much lately. My last 0.91 game there were only 4 prometheon spread across 1/2 the galaxy to be fought over by 9 different civs. So that's anything but plentiful.
Doesn't seem to be super-uncommon, but finding lodes of >1 seems to be pretty rare. In my current 0.92 game however, I do not believe I have any, so all the above posts might be onto something (Nebulula = common (along with all of the galaxy settings))..