I've been working through the SN in a non-standard order which Bhikkhu Bodhi recommended that essentially followed the four noble truths.
Here is an extract from an email he kindly sent me a couple of years ago in response to a query about how to approach the Samyutta and Anguttara, given that his sequencing of his Majjhima Nikaya talks and his "In the Buddha's Words" collection were so helpful.
I think the sequence he describes here is also discussed in his introductory material.
Bhikkhu Bodhi wrote:I suggest you might take [the Samyutta Nikaya] in what seems to me to be the original order, the most reasonable order, preserved better in the Sarvastivada school (in Chinese translation). In the Pali tradition, it seems, the books of the Samyutta were re-arranged and as a result one loses sight of the underlying groundplan. As I see it from the Chinese Samyukta Agama, this collection attempted, in broad terms, to mirror the pattern of the four noble truths. One should begin with Part III (of the Pali), 22-the Khandha-samyutta, followed by Part IV, 35-the Salayatana-samyutta and 36-Vedana-samyutta. These were to represent the noble truth of suffering. Then take Part II, the Nidana-samyutta. This represents the noble truths of the origin and cessation of suffering. You can also look at Part IV-43 and 44-which again relate to the truth of cessation. Then take Part V, just about all the chapters are important. This is called in Pali the Mahavagga, the large compilation, but in the Chinese Samyukta Agama it was called Margavagga, the compilation on the path; for it represents the fourth truth, the way to the cessation of suffering.
Thereafter you can take any of the minor chapters that catch your interest. Part I, the collection with verses, can be taken last. In the Samyukta Agama it was in fact put at the end, as a kind of supplement to the original Samyutta collection, but for some reason the early elders of the Theravada tradition moved it to the beginning, where it has effectively discouraged many brave souls who were intent on reading the Samyutta from proceeding further.
The Anguttara has no plan of organization apart from the numbers, and the only way to handle it is by reading it straight. But I would suggest beginning with the Threes and Fours and only then coming back to the Ones and Twos. These two early chapters very often merely list terms or permutations on a few ideas, and thus they can be more difficult to get a grip on them the chapters from the Threes forward.