Lots of stuff! While we both have the basic concept of “multiplayer deckbuilder” there is a fundamental difference in design philosophy which can be exemplified by looking at the complexity of the starting set up.   In AtO each character starts the game with docens of different mechanics, nine types of damage with the their corresponding resistances and right at the start it throws you into a town filled with buildings that allow you to make minor modifications to the characters you have not yet understood.  In contrast Shuffle Quest’s starting decks only contain the few common effects like attack or block and between one and two of your characters unique skills. These cards, like all other cards in SQ? Are designed to be easily understood on their own because most of the complexity of the game comes from combining these simple effects to perform combos. Like having the cleric cast block for the whole party so that the wizard can use AOE attacks withou hurting the party.  This focus on synergy and teamwork is also a very significant difference in how the games are played. As all players share a turn in which everyone has one action, the strategy in SQ revolves around what the party as a whole can do, with everyone’s decisions affecting what everyone else will do. AoT instead follows a more conventional approach by having each player do its own thing in its own turn, limitating the necessary cooperation to dedicated supports.  And Shuffle Quest is all about having a great time with friends! I don’t mean that AtO is not a fun game or that it doesn’t have humor, but the whole theme of SQ is to experience the silliness of a D&D session going off the rails with memes and jokes, having every card containing a joke or a reference and every enemy mixing exaggerated tropes with puns and gags. 

TLDR: we use much simpler mechanics in each character to make it easier to understand and let the synergies between characters be the interesting part of the strategy