In this thread there are many complaints about poor design of the interchanges - mainly at the larger stations so maybe it is complexity which stumps the posters - but few suggestions about alterations which would ease the lot of the average RailUK user.
I am not familiar with Stratford station on the Great Eastern nor with the Manchester stations, but I have used New Street, Paddington, Temple Meads and Clapham Junction quite frequently. Leaving Paddington aside as I use it for most of my trips to London and know it well having first been there around 195something, I have never found any difficulty in using any of them - I have never got lost in New Street nor missed my connection there. One can hark back to the late 1950s, early 1960s when I first used the station and was surprised to discover that it was in fact two parallel stations with a road between them. Then it was a real dump: bomb damaged, unloved, dirty and one really did have to go through ticket barriers to change trains.
Regarding Paddington in particular... I am finding it difficult to understand why one would want to change between a fast train, which I assume has just arrived, to a slow train which retraces the route of the train which has just arrived. Unless one wants any of the stations out to about West Drayton it is probably quicker to change at Reading to a Crossrail train or one of the Didcot - Paddington semi-fasts. In total there are four every hour.
Anyway, as soon as Crossrail is opened interchange from 'fast' trains will be simple: walk towards the buffer stops, pass the ticket barrier, turn right through the arches and take the escalators down. One can make the decision to travel east or west when one has reached the platform. Or is that too complicated?
There are two Paddington bike pens, one is on the site of the old taxi road and the other between Platforms 10 and 11. They are quite large, where else should they be sited? Putting one at the ends of the platforms on the circulating area (on the way to 'The Lawn') will not play well although it is in easy reach for the cyclists - whom I always assumed were fit and a bit of extra walking wouldn't hurt - it would rather screw things up for the majority of passengers who simply want to get to the Underground entrance or leave the building.
The bike pen is also easily reached from the overbridge at the western end of the platforms - this connects all the platforms and these to the taxi rank and Hammersmith and City line. Unfortunately, apart from the lift to Platform 1, only with stairs. But cyclists are tough...
Edit: Clarified that there are two bike pens.