You raise an important concern and measures of "energy return on energy invested", if done rigorously, capture it. EROEI for oil & gas is certainly lower than it was in the first half of the 20th century, when shallow wells yielded gushers. However, it's still far above the level necessary to provide the energy surplus on which civilization depends. That's more than can be said for conventional biofuels, even when protein byproducts are counted. As for the 90%, of course you're right that it's only 90% of produced energy, as distinct from the constant flux of sunlight and other background energy we take for granted, all of which provide services that we depend on. That doesn't diminish the importance of the 90% to the global economy. Someday it will be made up of solar, wind, nuclear, geothermal, biomass and other renewables, and fossil energy will be the tail, but we're still decades away from that point.