My husband hates those gloves, too, SadieKate. He gave me a pair last year that I really liked when I was riding a more upright bike, but then when I switched to a road bike I realized they were too small -- there is a weird tensioning around my little finger on each hand where the fabric just can't quite stretch enough, and it's excruciating. So he gave me his slightly larger men's pair because he had decided he didn't like them, and I had that exact problem you described with the pad on the thumb. I noticed that his were different from mine (a year older, different style) and had the padding in different places. His had a full palm pad and much more stuff around the thumb.
I just replaced mine with a larger women's size and I love them. They only have padding in a couple of places, kind of right where I need it, and it's perfect for me. He went back to his old Pearl Izumi White Line gloves, which I think are utter torture. I have a half-baked theory that it's a shoulder-width issue -- he and I have almost the same sized hands (yeah, I've got the giant man hands, no small-sized brake levers for me), but whatever weight is resting on our hands is coming at a different angle because he has much wider shoulders. I think I just made that up but whatever the reason, we have totally different taste in gloves.