Paradox said star systems would usualy have 3-10 things (not sure if they were including moons in that count). The Sol System is already over budget at 12 without pluto. That is my main concern with adding Pluto, it is a little bit unbalanced gameplay wise to have the human start system significantly larger than other systems. Like Paradox said, you gotta stop somewhere. If they included Pluto we would be having a poll about Eris and/or some jovian moon instead.
but the thing is that pluto is generally considered to be the official "end" of the solar system not including the little known kuiper belt dwarf planets of eris and makemake. and unlike other dwarf planets like eris or even ceres for that matter, new things are being discovered about it and just how quirky the planet is.
as for size yeah i can see why pluto would be omitted but lets face it, the Sol system while definately not a worthless system, it isn't El Dorado:
mercury is too close to the sun to safely exploit, so no go.
venus is a pressure cooker hellhole, so yeah, scratch that
earth has the only universal value as a habitable planet- except that we live here and aren't always the most reasonable people. (see: human history)
mars makes for a good, local, mining colony, due to its content of various metals.
the asteroid belt is hazardous as all hell and except for ceres, totally useless "
The total mass of the asteroid belt is approximately 4% that of the Moon, which is significantly less than that of Pluto and roughly twice that of Pluto's moon Charon (whose diameter is 1200 km)"
jupiter and saturn technically have the biggest financial value due to tremendous amounts of helium-3, though i can only assume expensive equipment would be needed to conduct mining since these are huge gas giants wiht some serious gravity wells, with jupiter being especially dangerous and radioactive.
uranus is actually the most financially sound planet for helium-3 mining since it has plentiful reserves and a very managable gravity well.
same kinda thing with neptune.
pluto while having little in the way of resources, holds
strategic value in being a jumping off point to leave the solar system (reinforced by the knowledge that warp drives in stellaris need to be far from the sun), being an outpost, and various other military needs.
so yeah, welcome to the sol system! where earth, mars, uranus, neptune, and pluto hold intrinsic values that don't require absurd operating costs.
https://en.wikipedia.org/wiki/Colonization_of_the_outer_Solar_System