I guess that still many PKIs are based on RSA which hampers the migration to ECC. Nonetheless, the SSH clients in some Linux distriubtions already prefer the use of ECDSA rather than RSA or DSA.
The main reasons might be the ones already said by Günther and Abdelhakim: RSA is just much older than ECC and thus more often used.
But I think that this is developing in the direction of ECC getting more and more used. Especially in embedded devices and for IoT stuff, ECC has just many big advantages over RSA. The key sizes and thus the encryption speed of ECC outperforms RSA significantly.
Regarding the answers that RSA is easier to implement: This might be the case for textbook RSA, which is of course super easy to implement. But for a real-life implementation, textbook RSA is also super insecure and there has to be a lot more work done for a secure implementation. Also, there are now a lot of cryptographic software libraries that should be used for bigger software programs (when developing not for embedded systems) and that provides good implementations of ECC (NaCl and libsodium are two that come to my mind).
Regarding the message expansion: I do not really get the point here. Even if a ECC 256 bit encryption expandes the message twice, we only get 512 bit, which is much smaller than RSA's 2048 bit. And that some (x, y) points are missing on a curve is also not problematic in my opinion.