Let me start by writing that I primarily play Orks in 40K and Orcs in Fantasy (10,000 and 5,000 points respectively). With that out of the way, I started a Space Marine army two years ago. I picked the Iron Lords chapter. The ultra sparse fluff about "containing the vile Barghesi" is what attracted me. I finally have a 3,000 point Space Marine army ready for local League gaming in in SoCal and crap, now I look
like "that guy" in picking an Iron Hands successor chapter with loads of Dreadnoughts, tanks and Techmarines. GW sucks eggs! At least GW didn't screw with the Il-Kathe craftworld army in the new Eldar codex. I prefer armies that are not commonly played.
most people go with cannon chapters cause you will be able to find the one that fits what your looking for with out much effort because lets face it, they have had 30+ years to make them cool. Other then like.. ward or some shit most peoples custom legions look like ass and ... they are just stupid. end of story.
Being able to create your own chapter gives you a levelling of modelling and painting freedom canon chapters cannot really apply. Plus painting one of 3-4 different black marines chapters, or attempting yellow sounds dull/horrible. I went with a greek theme for my space marines, then 6 months later Forge World came out with minotaurs. So I guess I play minotaurs now.