Your logic makes sense but the reality may not be as simple. Remember it takes time to pack, check out of hostel number one – then transport your stuff, find, check in, etc to hostel number two. If the two hostels are far away from one another, as I would assume they are, then you are possibly giving up a big chunk of a day to do the switch and I don’t know if what you’d get out of it would be worth the effort. I actually never have thought of doing that, to be honest. I’ll be curious to see what others think.

I’ve only changed hostels because of the hostel, not the location.  When I stayed in York, UK, I stayed in all three of the hostels. The first one was a IYH. There were plastic covers “pee sheets” on the mattresses- so when people tossed and turned it was noisy and there was a scout group there on top of that… so the next morning I moved to hostel number two… I can’t remember why I didn’t stay a second night at that one, I’ll have to check my journals. 

Both Berlin and Rome have good public transport. Ask for help and you should be able to get wherever you want. I agree with Keleti that the time and hassle of getting to the second hostel would not be worth it.

For any less than 5 nights in a city, I don’t think it would be worthwhile to switch logistically. But I think it’s an interesting concept.

I did it in Prauge, but not because I wanted to, because the hostel I wanted to stay at was booked up for some of the nights I was there.  So I stayed at a hostel on both sides of the Vlatava.  It definitly gives you a different perspective on the city though.

I’d just try toget a pretty centrally located hostel.  Packing up and getting checked in is going to cost more time and effort than a longer distance to the places you want to see.