In all honesty, unless you're there at rope drop, I don't think 40 minutes is out of line for Matterhorn. We were there at the end of January, and it was slow in the parks, but the line was always 45 minutes or more all three days we were there. Ride single rider if you can. You can select that as an option in Ridemax. That should help with Indy, too.
With the FP enforcement, there are only so many FPs you can get and use in one day. Getting there at rope drop helps a lot, especially on days with a 7 am MM or 8 am start. Single rider also helps a lot on Matterhorn, which doesn't have a FP and on Indy, so you can get a FP for another ride instead.
It definitely impacted the way we tour, too. But the Ridemax plans we made DID work. The software doesn't eliminate waiting, it just minimizes it. And even though 40 minute waits seem long, they are likely shorter than the standby line would be at other times of they day or shorter than the standby line would be for the rides it has you getting and using FPs for.