I have both the 40mm f/2.8 and the 50mm f/1.4. I think the 50mm f/1.4 can do a lot more, but the 40mm is awesome in it's own way (really small, and really sharp). Actually I find I'm using the 40mm more often than the 50mm on my 6D.
Of course a lot of that comes down to your style of shooting. I like the slightly wider 40mm for walking around with (possibly because I grew up with a 38mm film P&S), and the f/2.8 isn't all that limiting with the high ISO of the 6D. However when I want to shoot people, the 50mm f/1.4 just gives way more options in terms of the DOF control that lens can give you on FF.
Agreed. I also have the 50/1.4 and 40/2.8 for my 6D. The 40STM lives on my 6D, the 50/1.4 comes out for special occasions, i.e. darker available light shots, or where I need razor thin DOF.
If I'm using my 430EX at an event or party, I'll keep the 40STM on the 6D without a doubt. Shoot at f/4 with the strobe, and you're golden.