In regards to Bedwyn terminators they should go to Westbury as there are onward connections available there. It would mean you would need one less turbo but as it stands you still have Greenford, Banbury and Worcester still needing DMUs.
In regards to Stratford I believe the Paddington route was to serve Oxford. It would be good to see Oxford-Stratford return either with a FGW turbo or Chiltern, maybe as an extension of their upcoming Marylebone-Oxford?
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Re Stratford, from my understanding of FGW's intentions, it it not to provide a dmu shuttle between Oxford and Stratford, rather to run to and from London with a high-quality fast service aimed squarely at the tourist market, which suggests something other than a Turbo, and most likely operating off-peak, when tourists are more likely to be travelling and you could get your hands on an IEP or two. And if you were to have a 17.30 IEP back from Stratford (something which NSE/Thames Trains ran for many years), and get down to a two-hour timing, it would still be back at Paddington to cover a late-peak job out of London.
Further to my earlier post, thanks to the Network South East Railway Society's page of old Thames Trains publicity material and timetables, I have now found a 1994-95 timing, from Paddington to Stratford, via Oxford, using 90mph Turbos, of 2hrs 7mins, Which makes you wonder why Chiltern can't get there a lot faster in 2013, on a more direct route with 100mph stock. Current best looks to be 1hr 58mins.
Chiltern simply won't have enough rolling stock to operate the strange dog-leg you suggest. They are going to need every Mk3 and loco they can lay their hands on to free enough 168s to operate the Oxford service, and even then very tight turnrounds will be required at Oxford.
There is rather more logic in Chiltern taking over the Greenford-Ealing shuttle as it will soon become the last diesel operator in London north of the Thames. As for the Cotswold Line, no-one knows if dmus will still be required post-2017, and if they are, it's hard to see how they would get further east than Oxford, Didcot or Reading, to keep them out of the way of much faster emus and IEPs. And the need for Oxford-Banbury dmus will only be short-lived, thanks to the Electric Spine wiring scheme.