The good thing about anything open source is that it is easy for everything to be replicated and backwards compatibility is hardly an issue. Besides, it is highly unlikely that backwards compatibility would be broken with any well-defined standards. BIP39 is considered a Bitcoin standard and it is likely that it would be supported by wallets far in the future. Storing it in anything other than mnemonics is a hassle and highly unnecessary if you're concerned about compatibility; you'll be able to recover them easily even if they are not supported by Electrum in the future.

Electrum maintains compatibility with even their pre-Electrum 2.0 seeds. I doubt that Electrum would drop the support any time in the future since it doesn't hinder the development, just a nice to have. Tldr; Electrum or BIP39 seeds are both okay.