I don’t know much about Ignatian spirituality, but I would guess that a major difference is that St. Francis acknowledges or reminds us that we do not always feel God’s presence, but that even without His consolations we must continue to work at prayer, avoiding temptation, and living a truly devout life. St. Francis centers his teaching more internally, focusing on the “how-to”, so to speak, of living as God wants us to live, rather than on God interacting with us and being a part of those actions. St. Francis focuses on the individual works, such as developing a strong prayer life, keeping God as the focus of your entire day through constant aspirations, mini-meditations, etc. and recognizing your own weaknesses and how to strengthen them. Ignatian, on the other hand, seems, as I understand it, to center around how God is directly involved in your experiences.
Not sure if that’s a good answer. I love St. Francis, but am not so knowledgable of the other.