The -struct option of save saves each field of the structure as individual variables. Obviously for that to work the structure has to be scalar.
If you want to actually save the structure, then you don't want the struct option. To only save some fields, you'll have to either remove the unwanted fields or just copy the wanted fields into a new structure array. It's probably easier to remove the unwanted fields:
datatosave = rmfield(Data, setdiff(fieldnames(Data), {'Time', 'name', 'Version'})); %remove all fields but Time, name and Version
save('C:\danny\Pro', 'datatosave')