I successfully configured the Meraki VPN (on MERAKI MX100) with a shared security key and email/password for each user and native Windows client. But would it be possible to increase security using a USB authentication key or Microsoft Authenticator on a smartphone?
Not with just the native authentication. You need to either use radius or more ideally get licensed for Secure Client (AnyConnect) that will have a better end user experience
To add to @Mloraditch answer, I haven't done an AnyConnect+RADIUS deployment for 2 years now. Everyone wants SAML, because that allows you to natively authenticate against Entra ID.
And if you are using Entra ID, you can use a FIDO2 key, such as a YubiKey, or Microsoft Authenticator.