Word Bearers aren't an overly popular legion. I think they suffer from being quite stove piped. All WB armies seem to revolve around Gal Vorbak and being forced into Chaplains it really encourages it.
If you want a less popular legion, the ones that don't seem to crop up alot are:
(almost like most of their respective legions getting murdered at the start of the heresy doesn't inspire people to play them)
White Scars (Bikes are expensive)
Space Wolves (They have to take specific units and it seems to turn people off)
Dark Angels (But probably alot more common now!)
Emperors Children (Used to be super rare so I picked them up, but more common now they have transfers again and Tarvitz is likely to spark a renaissance.)
You should pick the legion you like the look and fluff of. People will tell you that some legions are good at doing X, which is true, but a legion isn't defined by what it's good at. All of the legions (bar a couple with specific rules about army composition - SW and WB) can do everything. If you want a Emperors Children jetbike list, a Iron Warriors jump assault list or a World Eaters artillery chain, go for it.
I've got a Sky Hunter EC list that has been really effective and the EC have no tactical benefits to playing as a Jetbike list. It'd be much better as DA or WS, but it can still be done by the purple ones.
I do get the thing about not wanting to play a popular legion. I recently picked up Salamanders for that reason over Night Lords after Book 9 made NL the flavour of the month!