Yes, if you compare fingerprints, then the important point is to authenticate both sender and content of the message. ‘Common Secret’ authentication as it is supported by OTR with Skype as the channel to negotiate that secret won’t be any good, nor will Skype text chat be sufficient to authenticate the sender of the message.
If it absolutely has to be remote, I’d go for a combined audio/videocall on Skype where one reads out the fingerprint and holds up a (ideally hand-written) sign with it – though I’d still prefer IRL-authentication (plus it’s more fun! :)), and ‘only authenticate keys in real life’ looks like a helpful rule-of-thumb to me.
If it absolutely has to be remote, I’d go for a combined audio/videocall on Skype where one reads out the fingerprint and holds up a (ideally hand-written) sign with it – though I’d still prefer IRL-authentication (plus it’s more fun! :)), and ‘only authenticate keys in real life’ looks like a helpful rule-of-thumb to me.