I don't like that buying elemental bullets not only increases the cost to buy the next bullet type. But also increases the cost to upgrade those other bullets. It feels like buying them in the wrong order would make getting upgrades too hard.
Also i'm not sure if it's intended that once you get dual bosses you can farm them relatively easily. Killing one doesn't remove them from future encounters. But you do get a skill point for them. This makes buying skill points seem like a bad choice in comparison.