I'm getting around the same rates. I had a steady gradual climb to 1MB/s for a 130MB file, which suggests that there are a lot of checks in the protocol that transfers data to the main memory. A workaround is to format a micro SD with fat32, and load books through the reader's card reader. I haven't pushed it, but I got all the way to 2.45MB/s before my file finished transferring.
It might also be a good idea to make sure the Kobo desktop app is installed on the computer you're using. I think I saw the Kobo desktop app copy drivers during the install. I doubt this'll make much of a difference in this case, but it never hurts to try.
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