I can evaluate some of it, but often times I don't see a spot on the wall to be patched and painted until the couch is out of the way, or a broken shelf in the fridge until all the junk has been removed. 

It would take very little time to patch the dents and do some touch up.

Painting over nail hole patches is not.

@Rachel Pivonka sounds like you may have found a good tenant who hit a financial rough patch.

I don't like the idea of leaving raised beds because the next tenant may not be a gardener & then you have a weed patch. 

Well, you could hire someone to put a patch in, or replace part of it, or if you think you can justify it - then replace the whole thing.  

We had a weird/bad patch where we had both units of a duplex (which had been newly remodeled), empty for a couple months.

However, a large number of holes in the walls or ceiling that require filling with plaster, or that otherwise require patching and repainting, could justify withholding the cost of repainting from the tenant's security deposit.

I have tried fixing things myself to save $, but if it is anything beyond paint or patching drywall, it takes too long.

They also asked me to patch a part of the roof.