I love this game! It so perfectly manages to encapsulate elements of both Isaac and PvZ. It has stuff for new players and veterans alike! I feel like there's so much potential with a game like this, as each run makes you do a different strategy. One thing that got annoying with PvZ was that you could just repeat the same strategy over and over and beat every level. With this game, I feel like you can make it so that every level has some unique enemies that force you to use different strategies.
One complaint I have with this game is that after completing the first loop of the game, you can't get new babies. It would have been cool keep picking new babies to try out new strategies, as right now the game is pretty short, and you only get to pick 6 babies total. It also feels like pills aren't that strong, and they become more of an annoyance than anything since you have to keep using them to get new ones, especially with the bad pills.
I think only having 4 slots is actually fine for a game like this. It gives each slot more weight and importance, and the player has to make tougher decisions and carefully select what babies they use.
I think having different characters that you can pick at the start of the run could be a cool mechanic to bring over from Isaac. Different characters could have different playstyles and start with different items. For example, Isaac could start with the D6, Magdalene could start with Yum Heart (an active item that gives 200 hearts when used), Cain could start with an extra slot for babies, etc.