I'm afraid that so much of this thread is regurgitated and years old.
Yes the fleet is a bit of a hotch-potch of liveries, but the number of redundant liveries is reducing. Gone now are the various shades of StanEx blue and WAGN cream, and the numbers of units in FGE grey or Silverlink blue are reducing fast. It's just a good thing that the Cl321s are sound underneath otherwise they could have ended up looking as tatty as the Cl315s did.
Part of that was due to dithering over branding and has since been undermined again with the loss of the franchise, but it has also been caused in part by the sheer size of the fleet. No other operator has had the same daunting task of repainting such a huge fleet. SWT, SET, Southern, London Midland and others have all had the advantage of brand new trains in the new colours directly replacing the majority of the fleet leaving just a few to be treated. Apart from the Cl379s, NXEA have had no new trains delivered.
Graffiti is an issue and is caused in part by the number of units that have to be stabled away from the main depots, the frequency with which they get back to Ilford or other locations where they can be cleaned, workload and, mostly, where the graffiti gets applied. Most of the stuff that remains in place for extended periods (including most of the tags applied to the front of trains) has been applied above the cant rail stripe which means it cannot be removed without an isolation, and this is something that the taggers are clearly aware of. While this can be done on a shed road at Ilford, there is only a finite amount of space in there and huge demands on the resources for maintenance and such. However, while cab front graffiti isn't necessarily dealt with very quickly, it does get removed eventually.
I'm not necessarily attempting to excuse the company, but simply to point out that operationally things are not always easy to achieve. Traditionally East Anglia has always been a bit of a backwater as far as the railway has been concerned with nothing much happening since the 1960s. All the money has gone elsewhere into more exciting projects with any improvements in East Anglia merely being as a consequence of the "trickle down" effect, even relatively recently. For example, the GEML has always been the refuge of stock displaced from the WCML and hasn't seen a brand new coach since the introduction of Mk1 rolling stock. There is a lot of catching up to do and I firmly believe that ANY operator would have faced the same challenges. Sure the branding and livery might have been a bit more consistent by now, but in what other ways would things be any different?
O L Leigh