But also by default, anything not in a black gem is not a mortal soul. How can using, for example, a troll's soul, a mindless creature that will viciously kill anything that comes near, be necessarily evil?
Point taken, but there is also one other difference between ammo and souls, trapping souls increases a skill you may not want to increase, picking up ammo does not. It′s rather silly that all of my friends who play Oblivion have a high mysticism skill yet only one of them actually took it as a major skill intending to use it. Really enchants can be a pretty big part of the game and they run out fairly quickly. Yes you also have to take armorer to keep your armor in tact but you can often finish a whole dungeon crawl without having to fully repair your armor. But viewing it from that perspective it may be silly to be fine with armoring but not mysticism but I′ve always found it weird that I ended up as a master of Mysticism by casting only one spell, it′s like becoming a master of alteration by casting your basic shield spell yet being better at casting water walking than a near master of alteration that honed his skills casting both water walking and a basic shield spell. With armorer it′s a little different since you only become better at repairing but nothing else.
Perhaps it would be possible to have a limit on how high you can level whatever skill soul trap will fall under ?