I'm going to put some (perhaps blind) faith in the promises of the Matrix 2 team, and also echo aktchi's feedback.

Cost per BIS mile would be a great add-on feature for MRers, and apparently pretty simple to incorporate.

Multiple departure/destination searches are also essential.

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Recently though, when I've used the month long search on matrix2, and I click on a date, there will suddenly pop up lower fares than the ones originally shown (sometimes on different carriers, which aren't shown at all in the calendar view). Also, some of these fares have really long layovers (80-90 hours), which are great as "hidden" stopovers, but I can't book them on any sites.

These fares don't show up in matrix1.

Is the matrix2 team aware of this? What's going on with these fares/searches?