Sounds good to me. However, one thing to remember is that it really will not be natural. No matter what, it is still a lined, man-made entity that will require maintenance. Even without fish, frogs and birds and plants produce waste.
I have a pond with fish (koi/goldfish) and a pond with no fish at all. The frogs don't seem to have a preference between the two, except for tree frogs- they like the still pond.
My reasons for building my main pond were similar to yours: Birds, frogs, plants... fish last. I love Koi, but my experienced opinion is that they belong indoors.
I get different types of enjoyment out of my different ponds. I have to say this, though- animals (no matter what kind) really do appreciate the cleaner water of my filtered pond. The birds visit the stream all day long.
(they do visit the unfiltered pond, but there is no running water there. I don't clean it very much and the water is crystal clear, all the time).
If you plan on having a lot of plants that float (lilies, etc), then a skimmer is not as effective. However, drawing oxygen- rich water through a skimmer to a biofilter is better for the biofilter. My "glorified plastic buckets" that I paid a lot of money for aren't any better than the glorified plastic buckets that I made myself. In fact, I'm pretty disappointed with my skimmer (400.00). I could have made a better one from a 40.00 slop sink.
I really love my mechanical filter box. It is filled with Black Knight brushes... I could easily fit another hundred into my system. But that is something you could make yourself, if you are so inclined.
Frogs and birds produce a lot of waste. I use a TT that I made from a large old flower pot, hardware cloth, and bio material.