We can see first of all a syncretism between the nominative and accusative cases in the inanimate declension which might be of some interest to people who have nightmares at night about object agreement and grammatical case like I do. While it's popular to derive the animate nominative from the genitive singular *-ós by way of ergative voodoo, I try to buck the trend in order to take advantage of a simpler explanation of the above pattern. It sometimes strikes me that these "ergative Pre-IE proponents" are simply intoxicated by the mere exoticness (or should we say apparent exoticness) of ergativity, seduced by a fashion that will some day pass (hopefully). In the global scheme of things, ergativity isn't exotic or rare; it's natural and common! So get used to it!
Anyways, back to PIE, the opposition between the animate subjects in *-s and inanimate pronouns in *-d can be quite satisfyingly compared to a similar opposition between the demonstrative stems *so-, likewise used strictly for animate subjects, and *to- used for inanimate subjects as well as for cases other than the nominative for either gender.
The fact that both *so and the nominative singular *-s are used only for animate gender is too coincidental to pass up. A deictic origin of this case ending seems painfully obvious to me and it surely is the simplest solution available by far. It however would then suggest that the nominative ending was originally optional for nominative subjects, being used more specifically to mark the definite subject as opposed to an originally endingless indefinite one. This solution works quite well considering that the pronominal inanimate ending *-d can likewise be sourced to the deictic *to- in somewhat symmetrical fashion. Adding to this, we should realize that the Indo-European accusative *-m is technically only the definite accusative case form since indefinite objects are often given other case forms (such as genitive, ablative, partitive, etc.) in many languages around the world.
If we factor in definiteness into the Pre-IE declensional system, we get the following structure that will hopefully inspire and enlighten. This is what I theorize for the Mid IE case system that preceded the PIE stage:
As you can see, I propose that the PIE declensional system originally specified definiteness for only animate subjects and animate direct objects. For all other cases (genitive, locative, etc.) and for all inanimate nouns and pronouns, definiteness was not conveyed by the case system at all. This then may explain the later pattern in the PIE system and explains how the nominative came to be marked when the tendency in languages is for nominatives to be unmarked. By this solution, I'm also suggesting that the case system was governed by an underlying animacy hierarchy of definite animate > indefinite animate > inanimate.
 For related information, read Woolford, Animacy effects on Object Agreement (1999), University of Massachussetts (see pdf).