I have observed that DML run faster on FEDERATED tables compared to SELECT statements.
FEDERATED isn't very clever when it comes to SELECT, it does not, for example, honor LIMIT clauses but instead of doing it on the remote server, does the LIMIT processing locally. There are other limitations to the protocol that FEDERATED uses that makes it sometimes underperform for SELECT queries.
This is not the case with DML operations as they are handled 100% on the remote server
Strangely not all type of select queries take long except where I use count() function.
Actually FEDERATED move all data to the client and then perform the count() in this case, and it would explain the lack of speed.