Well, I've been to both and to be honest, it would be a hard choice.
The beer was cheaper in Budapest if that helps
Culture wise, Berlin wins, you've got all the 'Wall' history, with parts of it still standing. Plenty of art if that's your thing, the New National Gallery was fantastic as well as the Bauhaus Archive, if anyone's into architecture and design. Eating out was very good value there too.
Budapest was great to visit, good prices for eating and drinking and there's a Unesco World Heritage sight at Fisherman's Bastion. You could also go bathing in hot thermal spring waters open year round (outdoor).
If you need any hotel recommendations for both Cities just ask.