I only ever run out of essence but I think that's because I like to craft and re-roll, so it's my own problem
Besides I can just use one of those scrolls that puts me back to X specific realm to collect the nodes from the floors, or use a +% essence mod on a few artifacts.
All the other resources are ok and I usually have too much power to the point where I just go to the power goblet thing and sacrifice the max it will let me (repeatedly).
I think it depends on the person and their gameplay style, IMO nothing wrong with the resource system the way it is. The game provides plenty of workarounds to top off a specific resource if one happens to get low.
ALso - on the note of drop rates for nether orbs, I have yet to find one and my creatures are close to 70 so I think they're still fairly rare, even post-patch. I will let you know when I find one for shts and giggles.
BTW - thanks for mentioning I need 4 particles of the creature I want to nether egg; I assumed I only needed 3 so I'll grab another one when I fight one. Cheers!