The character's thoughts are that since the soul has already left the corpse, a spellcaster should be able to animate neutral aligned undead (skeletons, zombies). They mindlessly follow the commands of their creator so their alignment should reflect that of their creator. They shouldn't just be NE by default, nor should casting animate undead be an evil spell.
Creating undead or greater undead of neutral or good alignment would be much more difficult. Magical effects exist that change alignments, so it seems to the character that with a great deal of research and effort, he could find a way to twist the weaves such that he can control the alignment of the undead he creates. To take it to the extreme, he is intrigued to see if he can create a good-aligned wraith, for example, that spawns good aligned wraiths...
I'd like to hear how the Eberron setting handles undead. I don't know if the Undead elves are all evil by default, and if not how do the rules work for non-evil undead.
From a gaming standpoint, I'd like to get suggestions on how to reflect these ideas. My DM, Al, is in this community as well. Al, I'd love to hear your thoughts!
For animating undead, I was thinking something along the lines of having to research a new spell that would be about fifth level that alows you to animate undead as the 4th level spell, but they are created with a neutral alignment by default.
Creating undead would be much more difficult. Creating neutral undead would require a metamagic feat, Create Neutral Undead, that would have a high spellcraft and knowledge religion requirement, spell focus Necromancy, and ... You would then be able to create neutral undead but the spell level is now 2? slots higher than that of the original spell.
Creating good undead, that would therefore spawn good undead, would be an epic feat. There would be epic requirements and the spell level would be 4? slots higher than that of the original spell.
Basically, my thinking is that nearly anything should be possible as long as the difficulty of accomplishing it is balanced correctly...