That is simply not the case. Yes there are some journeys over an hour, and there will be more of them when the Thameslink 2018 timetable is in full swing, but the average is not 50 minutes, far from over it.
Firstly a challenge. More than a quarter of current users are just in the core, and from 2018 that is likely to be a third or more. Why are these not representative? Indeed what is representative?
Starting with the Midland Mainline. The Thameslink stations north of St Pancras have around 40 million passengers a year. About 2 million of them use EMT from Bedford and the Lutons. Of the 38m left, 60% use stations from St Albans southwards. Most are going towards the core (with a notable flow to West Hampstead) and very, very few beyond (less than 1%). With a handful of station pair exceptions, all the London flows are less than 25 minutes, some are much less. The 10-20% that aren't going to London are usually making short trips - eg there are large flows from Elstree / Radlett / Harpenden to St Albans for schools. The average for this lot, including the non London journeys, is less than 20 mins.
North of St Albans, journey times are of course (mostly) above 25 minutes to London, but there's not as many of them, and times do vary. The faster TL trains to Bedford, which many Bedford commuters get if not on an EMT, are 50 minutes from St Pancras. Flitwick is 38 mins. Luton just under 30. And there's a lot of people doing Harpenden to St Pancras at, guess what, a little under 25 minutes. The average for this group, again including the non-London journeys, is a little more than 35 mins.
Taken together, then, the average for the north side of TL today is just over 25 minutes excluding the 'internal to core' passengers. Add them in and it's actually under 20.
On the south side it is more complicated for a number of reasons, not least the diversions away from London Bridge and the Southern routes serving many of the stations.
But, generally, the stations closer to London have much higher traffic than those further out. Post 2018 there will, for example, be an awful lot of people doing the hop Croydon to London Bridge on TL in 12-13 minutes. To take another example, Streatham has more than twice as many passengers as the entire Wimbledon loop (Wimbledon to Sutton exclusive). Even then a majority of people on the Wimbledon loop are actually only travelling to Sutton or Wimbledon (same goes for Haydons Rd to Wimbledon). Another one - Loughborough Jn (all Thameslink, mostly less than 10 mins to London) has as many passengers as Wivelsfield and Preston Park combined (shared with Southern, split directions). This all adds up to a lot of short journeys, which brings the average down.
Clearly, there are some journeys on TL that will be over an hour, indeed a very few will be over two. But they are (and will be) a small proportion of the total.
You can of course argue that the 700s are not designed for such journeys over an hour, and if I was feeling particularly benevolent I might agree with you, albeit in the same way that I might agree that a 450 isn't designed for a 2 hour trip from Portsmouth to Waterloo. However it would be very hard to argue that the 700s are not designed for journeys of up to 50-60 minutes, on routes where high capacity is paramount, and which accommodates 80%+ of all Thameslink journeys. That is what I think is representative.
Besides, it could be worse - you could commute from Richmond to Stratford, Amersham to Moorgate or Epping to Shepherd's Bush, all in rather less comfort than a 700.
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