I've been using DroneDeploy with S2.
It works pretty good for survey mission waypoint flying. They have a 14day free trial for the full DroneDeploy experience, then the app continues to let you fly S2 free afterwards.
It's not the best autonomous flight GCS I've used (for non-S2 platforms, e.g. Mission Planner, Pix4Dcapture, SiteScan, DJI GS Pro), and could stand to be optimized for S2 integration, but it is decent and has a slick, easy interface. It's really seamless and built for people that don't use Agisoft or Pix4D for reconstruction.
I haven't found any other free GCS apps to fly S2. I'd love to see something direct from Skydio with super tight integration.
If DD can do it, then the API is available and just needs someone with some skills to make a killer app.
S2 is ripe for Mission Planner (except it doesn't use Ardupilot). Someone contact Michael Oborne.
I definitely also noticed that... S2 takes off to about 10ft AGL then straight to waypoint 1. Mine went straight into a bunch of trees but luckily for S2's superior object avoidance, it noodled it's way out of the canopy. This happened more than once with DD on S2.
Actually, you can... In DroneDeploy app, open up 'Advanced Settings', uncheck 'Automatic Settings', then there's a slider bar to adjust the 'Starting Waypoint'. That said, it's very fiddly and only gives a subset of the total number of waypoints (which aren't numbered on the screen). Also, it seems like the app will reset your starting waypoint setting each time you adjust something else, so make sure to adjust it right before lift off.
Yes - And I think they are working on it... Because last week updates were released to Skydio2 app, DroneDeploy app, and Skydio2 firmware. All seemed to work much better together than the previous combination of apps/firmware.
My main complaints now are that
1) DD doesn't tell Skydio2 to come home for battery swap on multi-battery missions, and
2) the landing is seriously complicated by DD: It wants to auto-land but can be ~20m away from home. Also, it doesn't recognize the S2 logo for AI-assisted landing. And it requires some strange combination of halting DD-landing task to regain stick control, then turning off OA to actually land, but then stick control is gone again, which gives the effect of no control of S2 position between almost landing and headed to the ground. Feels awkward.
One strange NEW thing I noticed with the update is that the EXIF info on the imagery for Drone Yaw/Pitch/Roll now have a different name: Camera Orientation FLU Yaw/Pitch/Roll, which confuses Agisoft Metashape's importing of camera rotation data. Will explore further, but I'm assuming a software update on Agisoft's side will probably fix that.