In the evening peak at least, those extra trains to Crystal Palace will probably be the first to go as they leave a few mins after the main train leaves.

You're right about the long term benefits of being able to travel to Kings Cross and Farringdon without changing at LB or Whitechapel in the future, although spare a though for those existing passengers who use the Wimbeldon loop line. They're losing their through services which will terminate at Blackfriars and will keep the existing trains while it seems we'll have new Thameslink trains AND the ELL!