I think a fresh paint job makes a significant difference and repainting the trim white!

Phew, let see hereTaxes, when you purchase the property your tax assessment is going to go up (in Chicago they say pretty dramatically) so make sure you find out what the current property tax in your tax zone is, and apply that to the new purchase price.Move out costs can include but are not limited to such things as repainting, new carpet, toilet and sink repair, garbage disposal, trash out costs.

we have done spot or certain room repainting, but typically save the whole house repaint for between tenants time. 

As a landlord, you have to expect to repaint on some sort of schedule anyway (5-7 years?)

The apartments each used the same paint and paint color between move-ins and it was necessary to do a full repaint (one coat).

If you stencilled "No trespassing" onto the front door, and then repainted it when it was sold, that might do it.

It needs to have some of the siding replaced and repainted, the kitchen could use updating but not necissary. 

But over 25-30 years, I'll still have to replace again the roof, water heater (maybe on less time), repaint (maybe on less time) etc ...

I know that Hardie board does look better and is very durable but it will require to be repainted eventually and this is quite a bit higher cost.We currently live in one of the units and rent the other out and plan to live there for the next 5 years or so, then move to a different house and keep the 2-flat strictly as a rental; I expect us to keep the property for a good 20+ years.

You should charge for the drawer damage, damaged doors, nail hole  /wall patching, and pet damaged carpet you prorate the life of carpet..As for painting,, usually repainting is considered under normal wear and tear. but I charge for nail holes and wall repairs.