It sounds like the politics of TfE have contributed to today's mess, then. The potential wider scope of TfE aside, it should at the very least be ensuring integration, and that means branding as well as ticketing, and that in turn means consistent branding across the network. I understand the need for sub-brands, like Trams, City buses, East Coast buses, etc, and I understand the need to tweak liveries to fit different vehicle models, and change is not a bad thing per se, but they've failed in my opinion to present a unified image. Standardisation is an important element of usability.
TfL's wider scope aside, they have done this extremely well. Oyster perhaps gave them a strong incentive to do so, but nonetheless it's an example of branding that TfE should aspire to.