I think the basic system of spending science as a resource is fine. Apart from the player's natural curiosity it is the only thing incentivizing going to space in the first place and is at the center of the game's progression system as a whole. If progress could be made with just funds and time, the whole tech tree could be unlocked by just repeating the same contracts again and again.
I agree though that the current experiment system is a bit too simple. I think the different experiments need to have more specific requirements and challenges to yield results. That's why i think the Science Jr. is probably the most interesting stock experiment, it is very bulky and heavy compared to the other ones, so it is much harder to return it for full value.
Another example would be the impact experiments added by some mods that require you to bring a second craft along and crash it.
To then incentivize players to utilize all the experiments despite these challenges, maybe different experiments could contribute differently to each tech tree branch e.g. barometers would advance aerodynamics tech much more than seismic readings etc.
