In terms of emulation there is no difference between the two formats in terms of functionality, they are both simply "wrappers" for NCAs.
Although a lot of NSPs do use standardcrypto, XCIs exclusively use them, thus they would be the better choice, in cases where physical releases are a option. Eshop only releases naturally will be released as NSPs, and thus use title-key crypto.
I prefer XCI for many reasons, but mostly for:
Moving games whenever I want and delete updates/dlcs without the hassle to reinstall the entire game.
Note: IMO This relates to using a physical switch, but if they are both the same, then use XCI if you have an option?