The biggest advantage in Jatoba, for me, is that I have quite a bit of it. I have built several guitars from it, and found it is highly resonant and quite stable. The guitars it makes are loud and even aggressive, making the material quite good for professional performance guitars.
While I have never worked with Ipe, it seems to be mostly used for outdoor decking, whereas Jatoba is perhaps best known as a premium indoor flooring material.
HERE is a link to a Jatoba FT-000 guitar I recent took in trade-back and have for sale.