I can only speak for myself - I started off with 141 stuff at embry-riddle then realized what a waste of money it was and left. I more or less did most of my stuff part 61 at a local FBO and could not even begin to tell you how much money I saved. I am a big fan of local FBO's vs. 141 "Academies".
Simple fact is part 61 will save you money and you end up with the same little plastic card. The question of 61 or 141 did not even come up in my interview and I went through training just as well as the 141 Aeronautical Science guy next to me.