I (almost) completely agree with you, especially with beginners in mind. Although on a second thought, your approach might be a bit annoying for a bit more experienced players. There are people who played hundreds or thousands of hours only in career (and I am pretty sure not in the same save), and they would go through the exact same process again, and again. Of course, this issue kind of was in KSP 1 as well, but you could gather many science with analyzing samples on a planet or moon.
I suggest to combine both. Your approach could be a "main source of research points via exploration", but I would also allow players to gather science (or research points) with the "old methods" (or even "modernize" these methods, as I will try to give ideas later on).
There should be 2 main ways to gather science / research points: the exploration way, and the "scientific way".
The exploration should be the way to get the most research points at once (for example, the "first orbit" would give you 100 research points), and the science way would continously give you small amounts (for example, analyzing a sample would give you 20 throughout 1 month). The second approach has to give you really small amount, because you could have many "research labours". Maybe colonies could also research something, satellites would give you data that you could process to research points, and so on. I have not been thinking about any balance yet, but I think this way even if we can not avoid, but we could help the "just achieve the same milestones to get the same amount of research points every time" problem.
Maybe later on they could also add minerals to the game to analyze, build spaceships of (in career), and even a basic network of colonies and stations. The potential is unlimited. This does not mean they should make this game into a colony simulator, but I think giving the foundation to make mods (or expansions) that could be a huge hit (for a player like me who really enjoys these challenges).
Mods are a really, really big potential of this game, and I think the right way to develop the foundation of research gathering and research tree is to make it reliable and moddable, but also enjoyable vanilla.