As I see it, the problem isn't so much that your trays are emptied, then refilled with the powers you choose, so much as the game clears your trays, dumps in all of your temporary and prestige powers, then all of your primary/secondary chosen powers as blocks by powerset. If the respec added powers to your trays as you picked them, then added inherent powers like Rest and Sprint, then macros, then prestige powers, and temporary powers last, it would likely result in a much smaller amount of "where did that power wind up?" searching afterwards, even if it didn't address the overall problem completely.