I'm not surprised that Southeastern can't get their colour scheme's right. In fact, I can't think of a single thing they do right.
I think this is overly harsh. Southeastern are perhaps one of the most criticised TOC (maybe second after Northern) and often purely because they're a commuter rather than an intercity operator (and the fact that somewhat understandably you can never please commuters whilst the irregular intercity traveller is much easier to charm).
Apart from a couple of occasions, I have found most staff to be friendly. The only couple of issues I've had were with station staff. On the train, I've found all the guards (or "Train Managers" for HS1) to be good and helpful.
OK, they did remove the fast services via Tonbridge when HS1 was introduced, but the paths were put to good use with the additional Tunbridge Wells services.
In terms of train cleanliness and appearance, I have found that it has improved vastly. One of the first journey I took with Southeastern was from Beckenham Junction to Victoria (before I was a rail enthusiast) on an old 465 with NSE seat covers. The 465s now look much smarter and generally cleaner than they did then and the Electostars have had a decent refresh inside recently. With stations, some (Canterbury West for example whose subway used to smell terribly of urine about ten years ago) are much better whilst others still leave a lot to be desired (the Folkestone stations spring to mind).
I generally think that most train lengths are satisfactory on Southeastern (unless you're from Sevenoaks but I don't think any train could take the amount of people that seem to board there in the peak). If they were not, it would still not be the fault of Southeastern (unless they were deliberately under using their fleet) but rather that of the DfT.
The thing I'm most disappointed in SE over is the whole HS1 ticket routeing debacle and the automatic disapproval of tickets not thoroughly endorsed with the "Plus High Speed" mark. This is something which definitely should be looked into but probably won't be.
For the vast majority of cases, I think Southeastern does the best they can with the resources available.