Well since your thread's point is that EDO is too detached from the rest of the game, this comment seems quite contradictory, the issue now is that the exobiology loop also requires flying the ship? So the EDO gameplay should blend into the rest of the game, or not?
If there is something in EDO that is quite blended into the rest of the game is the exo-biology loop.
1 - Use the FSS from your ship in space to locate planets with biological signals.
2 - Fly your ship into those planets and use the DSS probes to generate the blue map.
3 - Filter the map to which type of signals you wish to look for and fly down to the surface.
4 - Either fly your ship at low altitude to look for stuff, or use the SRV. I prefer to use the ship, it usually takes about 20 seconds tops to spot the first plant pockets flying low over the surface. Once you pick a plant pocket to land / stop, you can usually already see more pockets of planets in the distance. I would prefer it was a bit more difficult to find, but at least it's better than the old quest marker arrows "special things exactly here!" we had before. The new system also spreads the POIs much more naturally across the entire planet, instead of having empty 1:1 planets with only a handful of small places with POIs.
5 - Disembark on foot or with SRV, scan the first sample. Either go on foot, or use the SRV, or use the ship to move to other pockets, depending on distance and how many pockets you can see from your location. If I can see the pockets I use the SRV, else I take the ship.
6 - After collecting all the samples (or scanning additional signals), run / drive back to the ship, fly back to a port, and deliver the samples.
Yes, exobiology is the most integrated part of the expansion, now if they could finish that off by making it so you can take atmospheric data (ground material) and get missions to sample stuff from the ship mission board, and gain ship materials while scanning planets, and gathering biological -and- "core samples" (perhaps using a new SRV) and rename it exo researcher (or a better name...), And taking the time to design mini games that fit contextually to the activities, while not making you feel like your playing a mobile game, they'd be getting there.