Electrum 2.0: non-BIP39/32 standardisation complicates matters immensely. Why?
Thomas Voegtlin , the developer of Electrum explains the reasoning in the first 10 minutes of this interview. I think he also posted same thing to Bitcoin dev mailing list some time ago.

https://letstalkbitcoin.com/blog/post/epicenter-bitcoin-69-thomas-voegtlin-electrum-spv-wallets-and-bitcoin-aliases

His main point against BIP39 is that it doesn't include a version number, and the requirement of the word list dictionary in order to implement it.