I think you use the 987F Pellon fusible, not the craft pellon, that stuff is way thicker. I made that mistake the first time I did a bag and found myself cramming it into the machine it was so thick.
So now I use the 987F Pellon and put a layer of shirt-tailer interfacing on the pieces too. It makes it a little thicker but not too thick. For the handles I just use the 987F no other interfacing.
I hate a bag that doesn't stand up when you put it down, so that's why I like a little bit of stiffness in all my bags.