DharmaMcLaren
Warlord
To borrow an idea from Fall from Heaven, you could have your units' weapons upgrade to the best available metal - they get a copper weapons, iron weapons, or mithril weapons upgrade when they're constructed.
Another system that could operate at the same time would be changing the way resource dependencies on units work. At the moment, if you have one iron you can train one swordsman. How about, instead of that, you train one 'soldier', and if you have one iron you can give him an iron sword upgrade (and he's then a 'swordsman' - I'm not sure if it's possible, but you could even make the promotion change the unit name). If you have two iron, you can train one soldier and give him an iron sword upgrade and an iron armour upgrade and get a stronger 'heavy swordsman'. The same principle could apply to other types of unit - give a fighter an iron spear upgrade for a spearman, iron spear and iron armour for heavy spearman; train a 'horseman' and give him a yew bow upgrade and iron armour upgrade for a 'heavy horse archer'. That might be a bit complicated to implement, but it would make unit production far more flexible, which would lend an interesting strategic element to the game - the strongest metals might not always be the most strategically sound choice, e.g. an archer with a yew bow, iron arrowheads, and no armour should be more mobile than one with a yew bow, iron arrowheads and iron armour; the former would be better for fighting a guerilla war against an invading army, while the latter would be better for bombarding a city during an invasion.
While we're talking about resources, too, I think a more realistic/interesting/diverse metallurgy system might be worthwhile. That is, if you have copper, you can make copper weapons and armour; if you have copper and tin (a new resource), you can make bronze weapons and armour; if you have iron, you can make iron weapons and armour; if you have iron and coal (a new resource, or perhaps marble to stand in for flux) you can make steel weapons and armour, etc. That way, a civ bent on conquest would increase its capacity for conquest as it acquired new resources, and on the other hand, a small defensive civ could, if it could obtain the right resources through trade or just a lucky starting position, fend off an attack from a bigger, less resourceful neighbour.
Historically, such differences in available metals were crucial to the expansion and decline of cultures. The Greeks suffered terribly from a lack of bronze during Rome's ascendancy due to depletion of their tin mines; bronze weapons and armour are actually more effective than iron and much closer to steel in effectiveness than iron. The Greeks lacked iron in abundance while the Romans didn't, the Romans used some of their iron to make steel, and that gave the Romans an advantage in equipping their armies. If the Greeks had had iron but couldn't have made it into steel, they'd still have been better off than if they'd been using copper weapons; if the Romans had has no steel weapons and showed up with only iron weapons and the Greeks still had bronze, the bronze armour and shields of their phalanxes would have been much better at deflecting the iron swords of the Romans.
You can see that it's far more complex than just copper vs. iron/bronze vs. steel; it's not just which metal you have, but which combination of metals you have that's really important. Tin alone is very weak, copper alone is weak, iron alone is weak, iron and tin is useless, copper and tin is good, copper and flux and coal is useless, tin and flux and coal is useless, iron and flux and coal is best.
One of the major reasons for the Roman conquest of Britain was to acquire its tin for bronze smelting, even with the availability of steel. The most dramatic example is probably the advantage that steel gave the Spaniards over the Inca - a few hundred conquistadors with steel weapons (and some horses) were consistently able to defeat the most successful armies in the Pre-Columbian Americas while outnumbered by up to a hundred Inca to every one Spaniard. A civ that lacked access to metals (as the Inca did) would be a terrible disadvantage compared to one that didn't.
That would set up a more interesting colonial dynamic, I think. If you were playing on a Continents map and you found your continent empty of metals, or with only copper available, or only copper and tin, you'd know that sooner or later ships were going to arrive from a civ with steel weapons and armour. Of course, the player would have the benefit of foreknowledge, and could thus plan in advance for the arrival of better equipped enemies (by focusing on light, fast, ranged units, for example), which the Inca couldn't until it was too late.
Since agrarianism seems to focus on efficiency of production, it could have an advantage over pantheism (if it needed one for balance) if it enabled buildings or improvements that slightly increase strategic resource yields - say, a shaft/pit mine on iron would yield more iron than either a standard mine or wildlands, or an industrial ironworks would grant one extra iron for every two or three or four available. (As a side-note, the Haya people of Africa provide an example of low-tech steel forging several centuries before Europeans were able to produce steel of a similar quality, involving the burning of mud and grass in an open hearth. That might be a good analogue for the pantheist method.)
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