That depends on what you do with the probes. I agree that replacing the current scan mechanics with probes would be pointless, but it should be possible to provide additional levels of gameplay using probes.
E.g. You scan the system as normal and then proceed to do a detailed surface scan, this could flag up areas of interest (lifesigns detected, unususual reading, high mineral concentrations etc.) , you could then launch a probe to further refine that area of interest and tell you what is there (What type of lifeforms, vulcanism, what types of minerals and % etc.). Another additional level of gameplay would be recovering the probes, these things shouldn't just transmit the data but you should need to recover the probes, even if this just uses the cargo scoop mechanic it would still require you to fly the spaceship and do something more than press one button. Alternatively a specific mechanic could be used to recover the probe, although that could end up being just another minigame and not really adding much.
Probes could also be used to allow us to interact with planet types that we can't currently land on. These probes could again bring back specific data on what's on those planets, such as biological samples, soil samples or data on Alien activity (if present). This data could then be used to determine whether or not some planets could be suitable for colonisation. Ideally this type of data could then be used to trigger other activities within the game e.g. If the system you scanned is close enough you could receive missions (once you've turned in the data) to return and take more scans, missions to bring scientists to the system, a community goal could be triggered to build a colonisation ship, the minor faction could provide combat missions to prevent other factions jumping their claim, other factions could try to stop the coloisation process through pirating supplies and so on. With a bit of thought that one discovery could be used to create a wealth of gameplay that could potentially encompass the entire playerbase.