I practice the Matsubayashi Ryu kata, and I have seen the Shotokan versions. There have been many discussions of the reasons/philosophy behind the changes made in shotokan kata. In general, shotokan seems to have lower, wider stances. In all the pinan kata, cat stances become back stances. The so-called "knife hand block" is also delivered differently. Matsubayashi Ryu, moreso even than in other shorin ryu styles, uses natural, shorter stances, and emphasises "whipping" power coming from the hips.
As far as the philosophy or conceptual differences, I think that will vary depending on who's teaching it. Like everyone, I have theories about why, in general, certain changes took place in the kata, but there's no point getting people riled up and protective about their style. I prefer the more relaxed and natural method of matsubayashi ryu to the "harder" way of shotokan. My style is more to use lighter footwork, getting off-center to apply redirections or grabs as I strike. That is my preferred application of the knife hand "block", (I see it as a strike, much like a crane wing/whipping technique, with the rear hand deflecting or grabbing as I wind up for the whip) I don't know if this concept could be applied to the shotokan version of the technique, if it is performed the way it is in their kata.
In general, my style is lighter on the feet, techniques are shorter with less winding up and chambering, and more close range grabbing, pulling, and bumping. I personally have other influences besides matsubayashi ryu, so my take and performance is not exactly what a "pure" shorin ryu student would look like...but really there's no such thing as "pure" karate.