FME supports the GML 3.3.1 core in common with GML 3.2.1. GML 3.3 is essentially an extension of 3.2.1, so it more or less adds to 3.2.1 and doesn't fundamentally change much of the existing spec. However, most new types that are only defined in 3.3 and not in 3.2 are not yet supported. If you have some sample data and schemas that use GML 3.3.1 you should be able to point to those schemas using the application schema mode. FME should read anything it recognizes and will ignore those types that are as yet undefined. If you have problems or encounter new types that are not yet supported, please post an example including the GML data, schemas and explain what specifically isn't supported as expected.