To be honest, I don't see what the problem is. Rochester, Chatham, Gillingham, Rainham, Sittingbourne and Faversham have 3 service back after midnight at 0117, 0144 and 0155. Ashford has an even more frequent service, starting with the 0041, then 0057, 0106, 0111, 0127 and 0138. All stations St Mary Cray - Charing even has a 0100 from Victoria. If you live East of Ashford, however, the last train with connections is the 2139 from St Pancras (2149 from Stratford). Miss that and it's a schlep over to to Charing Cross for the stopper, last service leaving at 2340 so no good for any late night events.
Does anyone know how busy the Ebbsfleet shuttles have been? Has there been a lot standing? Were 12-coach 395's really necessary for the shuttles? From what I saw, there were only a light scattering in each carriage. The only service I saw that turned out a considerable crowd was one that had come in from Faversham on Sunday night so I'm guessing an event had just finished. This was followed by lightly loaded services from Ebbsfleet and Ashford.