there are a few problems with doing a comparison in any profiler -
Take the tree view for example:
Stack traces change in the number of methods executed due to reorganization and also when when methods might be renamed.
Other changes include that if a profiler is being run when the computer is under different loads then this can affect timings due to the large CPU which other applications may be responsible for.
If we take the ANTS interface for example the method executions can happen at completely different times in the timeline.
The simplest solution might be to just provide 2 grids (similar to the All Methods grid), that allow some Diff comparison to show faster/slower times. This would mean that it will be total time spent in that method over the course of the entire application rather than just in a particular stack trace due to the issues listed above.
Back to your original question about comparison - Switch to the All Methods grid, you can select a region of time you are interested in to filter the methods if you want or just show all of them. Then select a row in the grid and do a select all (Ctrl + A), then copy (Ctrl + C) and paste into Excel. Do the same for the second results file and do all the diff's and comparisons you want from there. Not ideal I know but the best I can offer at the moment.
If you have any comments about the points I raised above then please let me know.