I've done the Madrid-Granada trip both by train and by bus. Sure, the train is much more comfortable, you can get up and walk around, etcetera, takes 4.5 hours and costs 66 Euros as of today.
The Alsa bus, leaving from Madrid Barajas T4 terminal (not sure WHERE you get the bus, though), takes you to Granada in 6 hours and costs 16 Euros.
So the difference between the two is 1.5 hours and 50 Euros. All depends on your comfort level requirements and/or your budget.
Saludos, MadridMan
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