Just book Berlin to Interlaken at whatever cheap price you can find at www.bahn.de.
A cheap ticket will be valid on a specific train to Basel then any onward train to Interlaken, no seat reservation necessary.
If you make this connection, you make it, if you don't you don't, and simply hop on the next train 30 minutes later, no big deal.
I had a 12 min stop-over at Basel and the train staff told me the usual story that it is the same station, but believe me, it is not as easy as it may sound. Specially if you are a first time visitor it is not so simple to find your way to the French side.
I had family with me and a couple of bags. We ran almost all the way to the other train but couldnt make it.
If you still want to risk it, here are a few tips.
1- You have to go in the direction of the France (direction in which your train is coming - from Zurich).
2- Go up the escalator
3- Turn Right
4- Go down the escalator
5- On your left between 2 shops there is a broad passage, turn into that passage.
6- In front of you, there will be a door (with if I remember clearly, a blue board on the top), go THROUGH that door (do not turn thinking this door is closed).
7- Turn left, walk a little and you will be on the platforms.
8- Find your platform (cannot help much here).
9- Remember, this must have been a border security immigration point before Schengen so the station is made that way, though the immigration counters are not used anymore, they are still there and can be misleading.
Bottomline: French regional trains are not the best. Donot have to worry about the reservation, we travelled First Class (as we had the Eurorail Pass) and it was 90% empty.
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