The issue was support for abortion on demand. There have been 43 million abortions since 1973. John McCain opposed the majority of those abortions. While stem cell research is an important issue, it isn't the one issue that should preclude a candidate from being considered pro-life. I believe George W.Bush doesn't oppose abortion in cases of rape, incest or the life of the mother. That equals a 96% pro-life record.
I believe most conservatives are pro-life and can accept abortion in rare cases. I would say being 96% pro-life is better then being 100% pro-death. Big Big Big difference.