@Vince, I think your analysis is pretty much spot on. It certainly fits with the frustration I feel over a lack of character and (ignoring the palace guard) no hammer units.
I see the Brotherhood as a small, specialised force with a proud cavalry tradition now desperately short on resources and forced to partner with a larger ally to survive. In this scenario, the core infantry units quickly become Basilean in nature with the ranks no doubt filled by ex - pats pensioned off from the Basilean army (ie veteran command). Some auxiliary infantry would retain the Brotherhood traditions, the villein bowman and villain penitents.
To boost the penitents I would suggest adding phalanx as with the bowmen. Pointed stakes are a cheap combat bonus for a disciplined but unskilled unit and I can’t see why a unified army would not make the most of it.
I’d like to suggest another infantry unit as chaff - war hounds or hunting hounds. These would presumably be common throughout the Brotherhood, and if you’re short on manpower you use what is to hand. The profile would be similar to gur panthers, fast and cheap.
I see the villein skirmishers as irregular light horsemen (border reivers, cossacks, etc) rather than part of the formal Brotherhood cavalry structure. This would be where the Brotherhood military tradition remains the strongest, and I would like to see the choice of units expanded to reflect this. I would suggest there levels; standard knights (paladin), premium knights (abyssal hunt) and a new category of heavy knights. These would be more like moving weapons platforms with a profile of Me 3+, De5+, no TC but CS(2) and Sp reduced to 6-7. This would fill the hammer role in the army.
Modelling these could be done by large, heavily-armoured horses and knights with polearms, greatswords or hammers. Or if you don’t mind straying into Green Lady territory, armoured bear riders.
I hope this helps; it was fun getting out of my system.
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