For Shepard's abilities, you are free to choose a reasonable set of powers that makes the most sense for her and that you would enjoy playing the most. As long as the changes between games are just game mechanics without a plot-related or character growth reason for the changes that doesn't match her canonpoint, there shouldn't be a problem. Just write her application with the particular powerset you would be interested in playing.

Please feel free to make the omni-tool make sense however you'd like!