The high cost comes propably with the idea, to not make new players try them for nothing, since they will rarely retreat. A lot of players think only in the 100% where you were good in an event, when you get the girl with 5/5 Skill and all 4 Slots. Getting the Girl itself is the biggest boost and also highest reward, the upgrades are icing on the cake. The 4 extra Skill Ups are merely ~10% which won't make from great to must have. The Equipment Slots would be a big possible power gain, but if you can barely make the ultimate mission, then you propably can't farm in the higher areas for the Wasp Raid Boss anyway. So you won't have enough Mid-Grade Seeds to get enough good equipment.
In the end, do what you can beat 100% of the time, other wise spend the Stamina elsewhere.