Maybe what we need to do is cobble together a new rule/power, similar to beast transformation, that would account for two consciousnesses occupying one body. Only available to humans, and including thing Like Dr. Jekyll and Mr. Hyde. Call it Alter Ego, and give it several levels to choose from.
Here's a simple way to houserule the most extreme version of this (that is, the less controllable MPD version):
* Make two complete characters. They can be as similar as appropriate for the character concept, or that can have completely different aspects, skills, and powers, within the guidelines below.
* Each of the two characters must have a High Concept that encompasses both characters. For example, one might have "Dual-souled <insert first description>" and the other "Dual-souled <insert second description>".
* If either character has aspects that reflect social flaws (for example, enmities, or opinions (good or bad) of other people toward the character), those aspects must be reflected on both character sheets without a good reason the social stigma changes. For example, if the two 'forms' have completely different appearances -- in which case one or both characters would need a power that allows them to alter their form, possibly in an uncontrolled way.
* In play, the forms are changed via compels on the High Concept. The GM can compel the change when appropriate (for example due to stress), with the player being allowed to buy off the compel as normal. Note that as with other compels, Fate is granted only if the change complicates the character’s life.
* As an option for characters who have some reasonable amount of control over their change, the player might be able to invoke their high concept to force a change. If appropriate, this can prompt escalation if the GM decides that the current soul might resist.
* When a change does occur, use the ‘mid-session power upgrades’ rules on YS92 to deal with refresh imbalances. Note that the character might have to spend Fate (and/or accept free compels) when changing to a more powerful form, even if compelled to do so. That Fate will be ‘returned’ when the next change occurs, of course.
Keep in mind that to maintain balance, the character shouldn’t be allowed to simply change forms at leisure; if so this would be potentially overpowered. This sort of house-ruled template should be used with extreme caution.