My experience has been that the weapon upgrades are extremely effective. This may be especially true because all fighting units produced in the province get the upgrade. A +1 to valor hasn't been that valuable for me. It might be because I tend to attack with a high rated general. One exception may be the units in Granada which are especially helpful for taking out the Spanish very early. Maybe there is more to it then I have figured out and someone else can help. Units with both armor and weapon upgrades backed by a good general are very powerful. Another advantage to weapon upgrades is that it helps Archers which don't necessarily need the valor upgrade if your keep them away from the enemy. You don't get them early, but when you do, glod/gold Parvinise Arbalasts are extremely good. Gold weapon handgunners can also be very annoying to your opponent.

Just my opinion...I could be wrong.