I think part of the thing I have with auras is there are already a lot of seeds in the game that purely add to the noise and need some balance. Aura's feel like they are just adding more noise to the background of things I don't really care much about. A normal run for me goes like this:
I try to stay around 10 crystals
I try to stay around 5 thorns
I grab any shield type seeds and keep them active
I plant maybe 1 checkpoint per zone when I remember
I stay on hearts otherwise and get as many as possible
All other seeds etc I ignore as they are not as valuable in most situations, and are actively bad in many.
All the shields in general I think are very very powerful, they greatly impact the distance of a run. They are just automatic takes and I always hope to see them instead of anything else.
For all weapons, homing enemies render them somewhat useless. Once the enemies are thick enough to justify using weapons in the first place instead of going around them, you have to keep moving all of the time to avoid the homing types. Moving into your own weapon fire is bad, moving away from weapons that need to be aimed is bad. Thorns take care of enemies in a way that protects you more in general, and is not possibly harmful to yourself.
So to summarize again, right now the starting seeds are all incredibly important, but after that I only care about shields, which make a huge impact, and any other pickups seeds/auras are mostly noise.
Maybe there are some types (especially of auras) or combos I haven't seen yet, but if they are that rare to get then I would say the vast majority of players will never see them.
Maybe the problem is thorns, hearts and shield are too powerful?
Like if there was a limit to 1 thorn, and a limit to 3 hearts, and the shields were only very very small areas and cost a ton, like 10-15, I would probably care about the other weapons a whole lot more.