Indeed.
The Hollywood image of Crusader armies in colorful surcouts is thoroughly fictional. Crusader armies had no uniforms.
The idea of surcourt uniform (at first plain, later with a stiched cross) started only during the 13th C. when the Knightly Orders of Holy Land (Templars, Hospitalier, Teutonic) began wearing them over their armors in reminiscence of the monastic habit (after all, they were monks).
You're right about banners & flags. And they mostly emerged during the Crusades too.
Up until the then, the only flags were ecclesiastical gonfalons (religious procession banners hung on a horizontal bar). The habit of taking a flag on to the battlefield was started by the Italian communes in the 10th C., who would bring their bishop's gonfalon set atop a portable altar mounted on an ox-cart into the battlefield. The altar was used to perform mass just before battle, the gonfalon flying above it a "reminder" of their hometown church (and so typically had just a simple cross or an image of the town's patron saint). During times of peace, the war gonfalon typically hung in the church.
The idea that "losing the flag" to enemy troops was a dishonor began almost immediately. If the flag symbolized the hometown church, by stealing it , enemy troops symbolically "pillaged" it. Thus began the habit of targeting the enemy's flag (and defending your ox-cart with your best soldiers).
[An aside: Since the war banners were ecclesiastical, it is not accidental that war cries from then on down to the modern era were typically invocations of the patron saint (e.g. the Venetian "San Marco!", the Genoese "San Giorgio!", the French "Montjoie Saint Denis!", the Spanish "Santiago y cierra Espana!"), rather than king or country.]
Ecclesiastical gonfalons on portable altars were used by preachers of the Crusades as they went from town to town. And then those very same banners were taken by them on Crusade. (The famous French "oriflamme" of the Abbacy of Saint Denis made its first recorded appearance in this role).
It was really only during the Crusades that they came across the idea of a battle "standard" (i.e. a flag hoisted on a vertical bar). The Seljuk Turk commanders whom they fought used spear-borne standards functionally during battles to indicate rallying points and bark orders across the battlefield. The Crusaders adopted this and brought it back to Europe. (Note: the Normans had used spear-borne pennons in battle before, but it wasn't widespread until the Crusades).
They didn't use their religious gonfalons for battle standards. Battlefield standards had to indicate which commander was where. That is when secular personal heraldry began. Initially, the colors or "symbols" they used on their battlefield flags were assigned arbitrarily pre-battle by the supreme commander, usually with no rhyme or reason. Just whatever was available.
(Interesting aside: there is really nothing "English" about the flag of St. George. It is actually just the flag of the Genoese ships which bore the English Crusader troops to the Holy Land. It was the only flag they happened to have at hand then.)
(Another aside: the Seljuks typically had depictions of animals on their standards to differentate commanders -- e.g. eagles, wolves, lions (which could still be found in the area). The Crusaders began using them too.
(Note: The Seljuks reciprocated; it was in response to the prevalence of crosses on Christian gonfalons that they looked for a simple religious symbol for Islam and came up with the crescent. The "shahada" (written statement of faith, as found in the modern Saudi flag) was sometimes used on their banners, albeit sparingly since it was quite unseemly for a phrase of the Holy Scriptures to end up all torn & soiled on the battlefield.)
This functional battlefield heraldry only morphed into personal, family heraldry sometime during the 13th C. The driving need here was the official seals of kings, dukes & counts. Sealmakers began carving intricate symbols into official seals in order to impress the illiterate and defy counterfeiters.
The choice of what particular symbols to choose for seals was drawn from the holder's name or achievements, including pilgrimages. Needless to say, religious pilgrimages were a big industry in the Medieval era and pilgrims typically wore a "badge" on their cloaks (e.g. the shell of St. James, if going to Compostela) to announce their purpose. It worked as a sort of passport during the pilgrimage; it differentiated you from vagabonds and other unwanted riff-raff, allowing you entry into towns & abbacies along the way. But upon returning, many pilgrims continued wearing those badges as a mark of social distinction. Even when the pilgrim passed away, his children continued wearing the badge.
When heraldry began in the 13th C., many families wanted to include these pilgrimage badges in their seals. And many coats of arms ended up sporting the shells of the pilgrimage of St. James. But there was no particular badge to indicate you or your ancestors had gone on the biggest pilgrimage of them all -- to Jerusalem, on Crusade.
That's when everyone suddenly remembered the eagles & lions used on the battlefield standards in the Holy Land. Consequently, eagles & lions became the badges of Jerusalem pilgrimage and spread like wildfire throughout European heraldry. Anyone who had an ancestor who had gone on Crusade had one or more of them in their seals.
Thereafter, rather than having them assigned arbitrarily just before battle, kings, dukes & counts began bringing their own pre-made battlefield banners, based on their official seals.
And Kamamura is exactly right. Making them "uniform" would defeat the purpose, since then you wouldn't be able to tell where each commander was!
And there was really no point in giving the troops uniforms. A commander doesn't need to know where his troops are. It is the troops that need to know where their commander is (or where the next rallying point is). And, as a grunt, your enemy is clear: anyone is attacking your commander or trying to stop you from reaching him (or his rally point). (And you know who your fellow soldiers are quite intimately after such a long march together.)
(Anyway, sorry for the long-winded & pedantic post. )
P.S. - In light of all this, I wouldn't mind an ox-cart-capturing "quest" for M & B (as I suggested elsewhere). Nor do I think it would be unseemly if spearmen did have colored pennons on their spears.
I wouldn't particularly mind a standard-bearer to accompany us in battle -- say, some lightly-armed fellow who will generally stand with the inventory chest and only move when we order troops to follow us (he follows us too) or to hold a position (he rushes to that position), as was indeed the custom. We could perhaps receive him only when we achieve some sort of "grant of arms" from our monarch.
