The only reason anyone thought DS9 and B5 were similar is because nobody else had ever really done a space-station show before.
Well, there's that, there's the fact that both stations have a single digit number at the end of their names and are positioned near a hole in space (wormhole, jump gate); both shows begin with a commander in charge and end up with a captain; both stations eventually acquire a starship (Defiant, White Star) in the third season of each series and both ships are eventually destroyed and replaced, both had story arcs featuring god-like good and evil forces (DS9: Prophets and Pah-wraiths; B5: Vorlons and Shadows); DS9 had Section 31, B5 had Bureau 13; both series had major characters lose an eye...
There are other similarities, but those I think are all of the most obvious. I chalk it up to coincidence, of two series beginning with a similar concept finding similar story elements that work. But the similarities are there, and it's more than just the fact that both series are set on a space station.
It's interesting, though, that no one ever accuses B5 of cribbing elements of DS9, particularly when it's clear how much Star Trek as a whole "inspired" B5.