You could try Cura.
Cura can print each part completely before moving to the next. The major caveat is that to individually print closely spaced parts, the parts cannot be taller than the distance from the extruder tip to the 8mm X-axis rods the extruder runs on, or spaced any closer than the external dimensions of the extruder. All this is entered into Cura as a setup. It all works pretty seamlessly.
Also, Cura output seems to be more efficient in general compared to Slic3r, which is not a very high bar in my experience.
Additionally, I have found that you can help mitigate the strangeness of Slic3r output by changing the dimensions of the model slightly to make wall thicknesses an even multiple of the extruded filament width. And also adjusting the number perimeters as well. Cylindrical parts can be infilled concentrically. All this in an effort to make as many continuous extruder runs as possible before the slicer deems it necessary to change tactics.
You don't have to do the math here, if you do not want to. Slice the part and look at the layers. Make adjustments, to the model within design constraints or to the Slic3r configuration, where the pattern gets weird.
Hope this helps.