YLM, I'm really impressed with the work you put into this. Not only do I recognize that the flaws you bring up are valid ones, but they're all issues that have troubled me in the past. One problem that I've thought of extensively is that this system places extra burdens on the DM. I considered a solution where the player herself takes control of the spirit, role-playing both a character and that character's opposition, but while some players would leap at the chance to try that, the credibility issues were too much to handle. I also thought about introducing randomness, but if that's ultimately what I go with, I'm going to need to be more careful than just making a list like the one you suggested.
Here's the thing: the punishments to the player need to be unavoidable. There should not be any incentive for the player to change her character just to avoid specific punishments (in your list, that would be a fire-resistant charging grappler). Any list at all would be too limited, unless it's large enough that its effects can't be accounted for. Even with an expansive list, being undead or a construct would probably give a player a significant chance of avoiding their own backlash, which is definitely not what I'm going for. I have yet to come up with a solution that works as effectively as having another person decide which effect occurs, though as you noted, that creates problems of its own.
So, we've established that randomness can deal with the first two problems you laid out. I initially considered that approach and rejected it, but you've made me rethink it, and it might be what I end up going with to some extent. As for the last two problems, focusing the effects on the player would deal with both of them, I think. Being the only one on her team being hindered by her effects will prevent her from being resented for her power or her ill effects. This was definitely something else that your system example did.
Over the next few days, I'm going to think about how to add the more random backlash element while minimizing the backlash's effect on allies and the player's attempts to avoid the backlash. Still, I have to stress that there are elements of this system that I like personally and would rather alter than discard. For instance, the role of the alignments in the system I set up. I like that it thematically presents every possible combination of aiding and harming. Having just two sets of effects, one for harming and one for helping, appeals to me in much the same way. These ideas lead to a single, alignment-driven presence that acts against the player, so it's natural that Spirit Magic ended up as it did. Balance is my top priority, as it should be for any new subsystem, but I'm going to carry these ideas as far as they can go unless it proves to be truly impossible to balance that.
By the way, I'm really glad that people are helping me with these issues again. Hammering this stuff out before I make the classes was exactly my goal in this discussion.
