While tree removal "might" retain the value of the depreciable structure, removing the tree does not really "add value" (in a sense) to anything. The cost has nothing to do with it. It's a deductible rental expense that I would probably call a maintenance expense.
Now you might be able to classify the tree removal as a land improvement. That would add to the cost basis of the land, and since land is not depreciated anyway, you would have no depreciation to deal with. But it would decrease any taxable gain on the sale of the land in the future.
Also, you got your understanding of safe harbor backwards. Those property improvements that qualify can be expensed if the cost is *LESS*, not more, than $2,500.
