The choice between the two seed formats will depend on your needs, all 2 options are safe and great, but I will mention some points from each mnemonic to help you with your choice:
1 - Electrum seeds don't have checksum as BIP39, instead, it's carrying a version number, this version number will determine whether the wallet is old (legacy) or segwit.
2 - Electrum seeds don't support nested-segwit addresses (p2sh-segwit starting with 3), however this type of address is falling into disuse, due to the bech32 standard already being well matured in terms of adoption. So this won't be a problem for you (I believe).
3 - Electrum seeds only have 12 words, while in BIP39 you can choose between 12, 15, 18, 21, 24 words (I think even more).
4 - Both electrum and BIP39 seeds provide support for
passphrase, a function that derives hidden wallets based on your passphrase, this additional password becomes an extension of your seed. It's therefore crucial not to lose both items, otherwise you will lose access to your funds.
5 - Electrum seeds don't support
BIP-85.
6 - Electrum seeds are recreated and recognized only on Electrum and Bluewallet, I won't go into depth because others have already answered this.
My opinion: I use both standards, the electrum standard is criticized because it has not been adopted by the industry like BIP39, so people can't import an electrum wallet into other apps, but this exposes your seed to risk, electrum is a wallet for desktop, this is the company's proposal (although it has a mobile app, but I haven't used it in years).
BIP39 mnemonic is accepted by all HW and wallets in general, so if you want to use your seed in other wallets (remembering that the more you restore in other wallets, the more your seed will be exposed), I like BIP-39 more because you can create accounts, this way you can use a wallet for each occasion, all protected by the same seed, whereas if it were on Electrum, you must create another wallet (seed) for each occasion.