While I like the idea of early corporations such as the India Company, I don't think they should provide commerce or food, and especially the first since commerce is a raw value that can be converted to science and espionage, and I doubt bananas and sugar should help with that. Also, such early corporations didn't function like modern ones, which are the ones implemented. So I think these (East and West India Company) could be national wonders (unlike modern corps) that would provide a city with a corporation a random resource between sugar or cotton (or corn), and spices or silk (or rice) for West and East India Company respectively; in trade for another resource the city has access to, much like Standard Ethanol and Aluminium Co.
I would agree with you that early corporations don't act as modern ones do. Certainly in the current incarnation of Civ 4 a trading company as a wonder makes more historical sense. However, I am in fact seeking a different sort of historical accuracy. I feel the greatest weakness in RFC's current representation of colonization is that (besides the occasional UHV) there is no incentive to attempt to build a vast colonial empire. Resources such as spices and cotton that once drove world history ("No, you dare not to make war on cotton. No power on the earth dares to make war upon it. Cotton is King.") are resources that are almost ignored by the prudent player. You need one for yourself, for a minor bonus, and maybe another to trade, if you're lucky enough to swing something you actually need from another power. Imagine using privateers to blockade Caribbean ports and getting access to the exporting resource. Imagine conquering the Incans and not being tempted to raze the cities because they're surrounded by mountains. Imagine conquering India and feeling that cities surrounded by jungle were still worth controlling for their resource wealth. Colonial powers were gluttonous in their pursuit of resources, they were not content with just one source and my suggested mechanism is just one way of implementing such motives into the game. There is probably a better, more historically accurate way to do it, but given the minimalist approach to RFC, the current corporation system seems the way to do it. I would change the corporations as such, assuming a starting date in 1500-1700:
Rare Metals inc: gold, silver, gems, etc. Leads to pure wealth. Available from the beginning of the game.
Luxuries inc: Spices, Tea, Silk, Sugar, fur, etc. Leads to pure wealth. Available from the beginning of the game.
Mining Inc: Iron, Copper, Coal, etc. Works more or less how it does now.
Textiles Inc: Cotton, dyes, wool, etc. Leads to production. Available with replaceable parts.
Foodstuffs inc (rework of Sid's Sushi): Wheat, corn, fish, bananas, sugar, pigs, cow, etc. (basically any edible resource). Leads to pure food. Available with refrigeration. This is how we can create the population explosion of the modern age.
Energy inc: Oil, Coal, Uranium. Lead to... man you could go anywhere with this one, let's just say raw commerce, maybe production too? Becomes available with Combustion. This is the big daddy corp at the end of the game that justifies your megalomaniac invasion of the mid-east, or... Norway?

.
Ethanol inc. As it is
Aluminum inc. As it is
The corporation system would need to be overhauled. Each HQ would be a wonder of sorts with a commercial benefit, but it wouldn't be a monopoly as it is now. By being the first to found mining inc. you don't establish a monopoly on the ability to turn iron and coal into production, nor are you able to profit every time anyone else anywhere else in the world does it (as the 5g per city would suggest). Every civ with the necessary technology would have access to the appropriate corporation, albeit at a cost, be it diplomatic or financial. The bonus food, production, wealth, or commerce (and probably some token culture) that would be generated would be evenly divided amongst incorporated cities. Instead of using corporations to increase every little colony's productive, growth, and economic ability (as it works now) you would want to keep your corporations at your empire's core, giving your biggest and best developed cities an edge. The occasional colony could be jump started by a corporation, but it's a strategy that would weaken the more it's used. There would still be a maintenance cost associated with corporations, but it would be much reduced as dividing the effect between cities decreases the need for an external limiting factor. You still have your stability pulling you to keep your empire small and manageable, but there's that incentive to bite off more than you can chew.
So how would this work? Let's say you start as France with no colonies. Just the normal Paris, Lyon, and Bordeaux. You don't have access to significant quantities of rare metals or luxuries so it doesn't warrant buying one such executive. However, you've started mapping the new world and you have managed to colonize the southern United States and you realize you've just discovered replaceable parts. It becomes clear that with your colonial access to vast quantities of cotton, and your dyes and wool at home (let's say you've got a city, or whatever you need for resources access in this new mod, on the sheep on Corsica) that it would behoove you to utilize the Textiles inc. corporation. The nasty Germans beat you to the tech and the great person, so you're forced to go to the corporation menu and fork over some hard earned cash for a few executives, but the (making the numbers up here) 24 hammers that your 6 resources will net you make it worthwhile. You drop your first executive in Paris. At this instant Paris is receiving all 24 corporate hammers that your nation is entitled to, plus (let's say) 3 just from the corporation being there. But Paris isn't your only productive center. Both Lyon and Bordeaux are well developed with production buildings. So you drop a couple more executives there, and now you have 24 divided 3 ways, yielding 8 in each city, plus the 3 from just the corporation itself. So that's 11 total in each city. Time goes by and New Orleans has been developing. It's also maxed it's production buildings and you decide to buy another executive (damn Germans), ship it over to New Orleans, and pop it in there. Now you have 9 bonus hammers in each of the four incorporated cities. This is good stuff, it's really helping you maintain your war machine in your war with the Germans, and you decide it would be advantageous to settle the sheep over on Australia, or conquer the newly independent city of Mecca (who's gonna stop ya?). You do both and now you have 40 hammers to divide evenly amongst your corporate cities, which are each receiving a total of 13 (10 + 3) from the corporation's presence in each city.
So how do I justify all this historically? The corporations across an empire represents that empire's ability to direct and utilize its resources efficiently, and in what direction the resources flow. It allows the player to designate an economic core area which will recreate the structure of a colonial empire. Most importantly, it will be a mechanism that helps create the titanic clashes between colonial empires that dominated history from the 16th century all the way to the beginning of the 20th century.