Reddit reviews The Annotated Origin: A Facsimile of the First Edition of On the Origin of Species

There’s an annotated edition of Origin that sounds like what you’re looking for: https://www.amazon.com/dp/0674060172/ref=cm_sw_r_cp_api_.zMWAbF957XX2

What, no Origin? I'd recommend this one complete with lots of additional information in the margins.
Good collection, though. Looks like you're another used-bookstore-scourer. :D

Without a doubt, yes.

Sure, many discoveries in the interim have revealed what Darwin never knew (genetics, DNA), but it is neither outdated or irrelevant. Nor will it ever be.

It is--and will remain--one of the most important books ever written. It debuts what many consider the greatest idea ever conceived by a human mind. Can it be dense, slow-going, downright boring? Yes. But it also contains passages that soar, passages of such lyrical beauty that I found myself nearly moved to tears. It is a book that reveals both Darwin's uncontainable enthusiasm for his discovery and the heavy gravitas of a man who knows the words he was putting to page were about to change the world forever.

Read the 1st edition; later editions include lengthy defenses and watered-down language. I would highly recommend an annotated version as well--having a contemporary expert help reveal the context or meaning behind the more obscure passages makes it a much easier read. I suggest this one: http://amzn.com/0674060172

https://www.amazon.com/Annotated-Origin-Facsimile-First-Species/dp/0674060172/ref=sr_1_1?ie=UTF8&qid=1521094773&sr=8-1&keywords=the+annotated+origin

$20.14 new from Prime. Used staring at $11.72

A much better version is The Annotated Origin by Jim Costa

See if you can lay hands on the one annotated by James Costa (or someone else, his is just the only one I'm aware of). My copy is just to the left of me. It's fantastic.

Comes in hard and soft flavors.