I believe PDFium is actually moving away from AGG towards Skia.
Using AGG might have been a decision from the Foxit days of this codebase, I wouldn't know.
From a user perspective, I can say AGG does its job at a very small binary size, whereas Skia would increase the size of built packages.
However, an advantage with Skia is, you can get an SkCanvas object rather than just a raster.
I imagine SkCanvas could be used e.g. for PDF to SVG conversion, which an AGG build of pdfium can't do. Haven't actually tested this yet though.