There's a downside of using electrum seeds, at least if we're talking in the long term. Electrum seeds, as said by their name, can only be generated from electrum. But, BIP39 is a proposal and many wallets adopted it. Electrum doesn't propose anything, the developers simply believe that their way is the proper one.
How sure can I be that electrum will exist in 10 years from now? A lot, but I can feel more sure with BIP39.
Electrum's method is fully transparent and it is only a difference with generating the seed for use with BIP32. You can always derive your private keys with Electrum seeds and there really isn't any obvious disadvantages.
Conversely, would you rather continue using a standard that is "Unanimously Discourage for implementation"? BIP39 is only used because it is proposed in a BIP. Just because there is a proposal for it, doesn't mean everyone should use it. It's almost like having a BIP for increased block size... It got rejected at the end.
It allows you:
What version of Electrum are you using?