If you have a different pen name for every series, you lose the benefit of crossover, which is what keeps your backlist alive. Whenever I run a promo on my newer, PNR series, I see an uptick in sales of my older, SFR series, and even my fantasy romance series, despite them being quite different.
If you write in vastly different genres (eg romance vs thrillers) then a pen name is a good idea, but if it's just different flavours of the same genre I think you're doing yourself a disservice and losing sales by separating them.
For branding, you want to look more at the themes of your writing than at the stories themselves. If you're a sci-fi writer, are you better at technical details, or space battles? If you write romance, and your heroes bad boys or nice guys, or do your heroines stand up for themselves? Those are the things that will make readers cross series, not your heroes occupation.
Then brand your series covers to play up on whatever hook that series uses.