One of the biggest grips for Southern commuters when the 442s were introduced on the Brighton line were the doors. These are end-loading carriages (i.e. the doors are at the end of the carriages in normal mark 3 style), as opposed to the usual more central-loaders that we are more used to - 319s and 377s. On a busy train (especially when gangways are blocked with standing passengers) the loading and unloading at stations can be painfully slow. It also clumps passengers in close groups, as opposed to spreading them more evenly down the platform.
So, I would say that the central loaders are considerably better for busy routes with large volumes of passengers and frequent stopping. They help channel passenger movement more evenly in the carriage and onto the platform.
Your point about longer journeys may be valid, but the vast majority of the journeys on these trains are relatively short - less than 1 hour. Certainly in the context of have refurbished 319s running on the GWML, I don't think that would be a huge issue.
The biggest issue with the 319s is the seeming lack of care about them. They are often scruffy, and have a poor ride quality - especially a higher speeds. They are also old - by the time the new Thameslink trains come on stream, the 319s will be pretty much 30 years old; and they have been 30 very hard years. I'm sure a full refurbishment would improve this, but I'm sure any Thames valley commuters who saw these and heard the suggestion thay may get this in five or six years time would not be too happy...irrespective of the total rebuild they would need to get them up to scratch.
The lack of gangway through the driving cabs is also an issue, which does not help with evenly spreading passengers throughout the train - no co-incidence that the 377s do have this feature, but for me it was an odd move to block them off on the Southern 455s. You often see an 8-coach train (particularly on the South Eastern section, whose entire suburban fleet lacks gangways through the cab ends) where the front 4 coaches are absolutely rammed and the rear four have available seats.
Edit: Lots of typos!