I personally prefer Smart-ID because of the low friction in getting started, compared to Mobile-ID where you have to get a SIM-card that supports it.
The security assumptions for Smart-ID are far weaker than MobileID or ID-cards and actually no government institution will accept such signatures. You can sometimes use it for identity, for example the Tax Board allows you to authenticate via your bank, which in turn may support Smart-ID: https://www.emta.ee/eng
Since offering Mobile-ID actually costs a lot of money to banks (since there is no direct connection to the card via browser and a USB cable, you have to pay to use some API-s across SK.ee & telcos), it is the main motivation for developing it.