My few ideas after playing the game (and still going)
1. Soul Hearts and Blue Baby - What if soul hearts are temporary hearts which gradually goes down and you can only get them from enemies just like coins, which are used first for the babies, and a character like blue baby would be nice with this mechanic he can't use red hearts and Little C.H.A.D. and red hearts that drops will turn into a soul heart instead, but he gets double the soul hearts.
2. XL Room - What if just like in The Binding Of Isaac there's a chance to get an XL Room but instead of forcefully making you stay there you can choose whether you want a normal room or the XL Room and it will have a bigger room but uses 2 rooms and you get to choose 2 rewards instead of 1.
3. Hidden Rooms and Shop - What if every floor has a chance to have a hidden room which gives you a few coins or a shop which will activate after the level and you can click on him if you want to see what babies he's offering or sell the babies you have.
4. Devil Deals and Angel Room - What if you don't lose any of your babies (except in the boss room) and you get an angel room or devil deal and you can use the shovel on the babies that you think might die which will not count as losing a baby so that it's a bit more possible, and once you finish the boss instead of the normal items you get an angel room item or devil deal.
5. Pills - I know pills is already in the game but what if pills work for enemies if you give a slow pill on an enemy (except the boss) he would go faster and a speed pill would make him slower and a power pill would make him have less attack and a full health pill would make him more vulnerable.
Few more pills:
1. Bad Gas (Good Pill) - Baby (Knocks back the enemy in front of him) / Enemy (Poisons the enemy including the boss)
2. Bad Trip (Bad Pill) - Baby (Half's the health of the baby) / Enemy (Fully Heals the enemy except the boss)
3. Telepill (Bad Pill) - Baby or Enemy (Teleports to a random area except the boss)
4. Paralysis (Bad/Good Pill) - Baby or Enemy (Paralyze enemies or babies except the boss but better than freeze because it would work for stone enemies)
Oh yeah the feature I'd like more than anything right now co-op
6. Co-op Mode - What if you add a co-op mode. Players would share coins and hearts but the main player (host) controls the active item and the pills (possibly also cards) and half of the babies while the other player only controls the other half of the babies, and the players get to choose which passive items they want by buying the item first.
7. The Lost - He doesn't use any hearts and heart producers, but has no chargers (but instantly kills the first enemy and can be recharged after the boss) and all babies have a longer cool down depending on its original price.
Just few of my thoughts maybe it's good, maybe it's not, I just can't wait to see what the game will have.