This is the real problem with resource distribution. Sure, it'd be nice if a player without Niter would go and take some Niter from the guy that has it. In practice, though, the player with Niter is going to have stronger units than the one without and war is almost a non-starter. Instead, the player without could try to trade for some Niter. But, the player with would probably be smart not to trade away that Niter. So, if you're lacking a critical strategic resource, you usually just have to wait until the next era and hope that have you the next resource. Every Civ game has been like this, though.
Isn't there an option to evenly distribute resources during the advanced game setup screen? I can't check from work.
Well, there is a reason resources appear before the units that need them. I admit it is a small time window, and you may be out-teched, of course, but there it is. Aside from having to resort to “regular” non-resource units, too. (And pillaging the resources your enemy has before conquering them, too). That’s what strategy is about.
You coud also tell nobody shoul run to far away in the tech tree, as to recover you may need to work or reduce its research power by resorting to war, and he has stronger units because he is several techs ahead. Of course, and indeed, this becomes boring and frustrating sometimes, but other times leads to very satisfying and remarkable underdog epics. For me, this increases considerably the game replayability.
Of course, there are things that can be improved. With numeric resources, pillaging could give you some amount of the strategic to keep you going, maybe it could be worked on too if you could scrap some resources from killing units that use them (maybe via military policy or other enabled ability).
@heinous_hat has a point resoure clusters are more of a problem in small maps than in bigger maps where you have more places to expand (note that, barring exceptions, late game strategics tend to appear in zones with not that big appeal for settling: desert, tundra, ocean) and more trading partners. So I concur with him that maybe adjustments should be considered depending on map size, and also an advanced setup scroll would be neat).
From there to shouting everyone in the face this is a gamebreaker problem that needs to be solved asap there is a stretch, tough.
