If one purchases a house/apartment in middle of the year, thus the mortgage payment - and deductions - are for just part of the year, shouldn't one be able to pro-rate the "eigenmiete"? I've heard you need to include the entire amount as income, but it makes no sense to me.

Is any portion of the "nebenkosten" deductable?

Not your utilities, no. But any repairs to "fixed items" in your house (or replacement of like for like in case of a breakdown/end of expected lifetime) can be deducted. Anything that you do to improve the energy efficiency of your house can also be deducted (generally 50% if it is not replacing something equivalent). If you do not have many repairs there is a fixed value that you can also deduct without having to provide back-up docs. Most of what you do to add value to the house which is not a straight repair or replacement can only be deducted when you sell your house and start working out whether you owe property gains tax.

i think it's pro-rated. When I did the first tax return after moving to my place I put the full amount in. When I got the final assessment, the Eigenmietwert had been reduced (less tax for me)