Glad you asked! You will be able to customize your character in a number of ways. Aside from Skullcaps, which modify gameplay in many different ways, you will be able to attach attribute modifying body parts, similar to armor pieces in more traditional RPGs.
Body parts will alter your base stats such as attack range, damage, base health, speed etc to let you compliment your play style. If you choose to play as MaryAnn (or other playable characters, stretch goal pending!) your starting attributes will be different. You collect body parts like traditional loot - but if you die, don't worry, you get to keep them. We will cover this more in a future update.
In terms of replayability - oh my gosh this is what the game is all about. We are PACKING FranknJohn with content. Skullcaps, Body Parts, Dr. Harmins Journal Pages, secret rooms, hidden narrative, multiple endings, unlockables, achievements, you name it. Part of the excitement of working on FranknJohn is the no-holds-barred approach to content creation.
Also, something we are experimenting with, is adding new content into the random generation pool as you play more.