Why did I know you were going to be the first to post in this thread!
Regarding the Berry bushes they're only complex if you start to 'Farm' them, otherwise the Wild bushes will still be in place providing a regular basic food source for a new player. It'll just mean every few days you'll have to do some running around.
I think the main benefit of the new system is that it prevents 'fire & forget' planting of cuttings. Which is basically what we've had until now, by being allowed to relocate entire vineyards of fully formed bushes en masse that required zero maintenance. Up-front costs would do little to change that dynamic, except perhaps delay it a while.
That could change in the future, but are you suggesting more complexity?
I don't see a way around this given the current storage system. Maybe if in the future the game moves toward a system of Max weight storage rather than the current Slot based storage system it would enable a greater amount of 'light weight' items like cuttings to be carried.