It sounds like you've had a pretty rough time with ATG, Amber. I'm sorry to hear that. People's reactions to it can be as individual as their conditions going into it. Some have difficulty tolerating it, while others, like my husband, pretty much sail through it. I am so grateful he has never become severely neutropenic.
My understanding of the cytoxan protocol, however, is that everybody becomes severely neutropenic because it basically obliterates your immune system and waits for it to regenerate on its own. This tends to be a longer and more difficult process than ATG, so any difficulty with ATG should not be seen as weighing the scales in the other direction.
The main attraction of cytoxan, of course, is that it offers the possibility of a complete cure rather than just remission. I say "possibility" because, as we have seen, even people who have had transplants can relapse. The advantage of cytoxan alone without transplant is that you avoid the GVHD issues, but without any donor cells to fill in the void, you are going to be vulnerable to infection for some time. Naturally, they're not going to send you home shortly after treatment the way they may with ATG. Expect to be in hospital isolation for a while.
None of this is meant to recommend one treatment over another, just some things to think about. There are pros and cons to each one, and the best thing to do is talk to the doctors that would be doing each procedure and go with what feels right for you.
-Lisa, husband Ken age 60 dx SAA 7/04, dx hypo MDS 1/06 w/finding of trisomy 8; 2 ATGs, partial remission, still using cyclosporine