Rework red babies-only challenge so it requires to place only red babies instead of having only red babies in the deck. It sucks when you get a little unlucky with the 4/5th red baby so you couldn't complete it 

The Black Bean = too pricey for such situational effect, especially as it's only for close placement and effects only once per baby. Either needs lower(33) price or other mechanic of use, say farting attack for defensive babies(then 99 price justified)

Wind-Up Key = who would want to use that, when chargers are super valuable?! I propose change: one use per level, manual launch of 1 charger, and next level charger would be back on its place.

First off, I'm really enjoying the game. It's great. However, I feel like the heart limit in latter loops really limits the potential for new babies and think that it should be changed somehow. 

Secondly, while I do think that limiting the baby pool so that any babies that you've seen before can never show up again is fine in theory items like the D6 and More Options practically become a disadvantage by making it so you get less babies in the long run. I'd suggest either changing how this mechanic work or making More Options into a tier 2 item that also allows you to pick babies that you've already seen a second time.

Haven't read the entire thread so maybe someone already suggested similar stuff but here's my baby suggestions:

Blaster Baby: Works like the Cob Cannon from pvz1, very expensive, looks like the Blaster enemy from isaac. Charges with a bomb fly after some time which you can shoot whenever and wherever you want.

Big Fan: A defensive baby that can fly upwards and prevent enemies from flying over it, not much to it.

Lil' Swarm: A swarm of flies that works like the pumpkin from pvz, it can be placed on top of other babies to protect them and comes with 10-12 flies. Each time it gets damaged a fly get's removed. Whener x amount (this'd need to be balanced well) of enemies die an extra fly is added. Could also add the swarm's blue fly mechanic to it and make it so the flies turn blue and deal damage too? Would depend on cost.

Intruder: Works like a threepeater from pvz but shoots twice in its own lane. Alterntively, instead of the double shot, it could have a slowdown effect instead. Would need to be pretty expensive.

Lil' Portal: A limited use baby that can either redirect portals when used in the Ark or spawn its own portals if placed on an empty tile. Enemies that warp through those portals also take some damage.

Bum Friend: Takes coins in exchange for pills. Simple enough, not too good early but should come in handy after you've emptied the shop. This could alternatively be an automatic coin collector.

Dark Bum: Automatically collects hearts that you haven't collected instead of letting them fade out. Spawns attack flies in the lane or pills in exchange. This could alternatively be an automatic heart collector.

Tinytoma: Alternative to the swarm, another pumpkin-like baby. Place on top of other babies, splits as it takes damage, deals damage when it splits and releases attack spiders when each part dies.

Tough Baby: A bumbo with brass knuckles, works like Bonk Choi from pvz2. Could sacrifice the ability to attack backwards for a chance to make an empowered attack with a tough love-like effect.

Hungry Soul: When placed creates a crack on the floor, whenever an enemy steps on the crack the floor opens up and a ghost comes out to bite and deal damage. This could either work like a chomper from pvz equivalent, making it so the ghost has to chew after biting a zombie, or a more original baby that, after placing the first one, any further placements on empty tiles will only place the floor cracks. This'd make it so that the existing baby can move in between floor cracks and attack enemies, the ghost would be immune to most things aside from explosions but there'd be a limited number of them. To add an extra ghost you'll have to place a Hungry Soul on an empty floor crack. 

Lil' Ladder: It's the lightning reed from pvz. That's it...

Gello: Places a Vis like baby that shoots out Gello at the nearest enemy and makes the funny whip sfx. The whip has limited range but if it hits an enemy and the enemy doesn't die Gello will hover above them and shoot while following their path. If it kills an enemy it'll just get ready to whip again.

Dirty Baby: A defensive baby that creates dips on adjacent lanes while it's being damaged.

Prism Baby: Similar to multidimensional baby but makes shots that pass through it duplicate to adjacent lanes.

Robo Baby: Shoots piercing technology tears that deal little damage but go through everything. You can stack another Robo Baby on top to make a 2.0 Baby that shoots tech 2 shots, that don't pierce but deal high damage.

Penny Sack: It's a pvz Marigold and creates coins, if you have a free slot this is a good pick.

Lil' Brimstone: Another expensive baby that I feel HAS to be in the game. Charges up a brimstone blast but won't let it loose until you click on it. Simple, deals a lot of damage ticks and pierces everything. The main drawback is recharge time.

Incubus: Imitates the shooting style of the baby directly below it.

Lil' Horsemen: Becomes a headless horseman upon placing. Can change into other horsemen depending on what pill is used on the baby, doesn't get any extra effects from pills. Each horseman shoots different flies (locusts) in the lane.

   Options:   - Lil' Famine: Requires a speed down pill. Shoots slowing flies.

                          - Lil' Pestilence: Requires a full health pill. Shoots poison flies.

                          - Lil' War: Requires a power pill. Shoots exploding flies that deal fire splash damage on adjacent lanes.

                          - Lil' Death: Requires a percs pill. Shoots death flies that deal heavy damage to a single target.

                          - Lil' Conquest: Requires a speed up pill. Shoots multiple flies at once on its lane. 

                          - Headless Horseman: Use a speed down or something's wrong pill to return to this version. Shoots regular flies.

Lil' Spewer: Another pill based baby. You can either introduce a creep mechanic or just make it shoot tears, I'll keep it as tears here tho. Starts as regular spewer with brother bobby shots and changes according to pills. 

   Options:   - White Spewer: Requires a speed down pill. Shoots slowing tears on adjacent lanes.

                          - Green Spewer: Requires a full health pill. Shoots poison tears on current lane.

                          - Red Spewer: Requires a power pill. Shoots strong red tears on current lane that split into two on adjacent lanes upon hitting an enemy.

                          - Black Spewer: Requires a percs pill. Shoots splash slow tears on current lane.

                          - Yellow Spewer: Requires a speed up pill. Shoots number one tears, with high speed but low range.

Clot Baby: A single use baby ala BBF. When placed begins to burst and spawn lil clots until its health runs out. A cheap iption for quickly getting charmed/friendly moving characters.

Succubus: Like Hallowed Ground but increases damage and deals damage to enemies in its range.

Holy Water: Single use baby, turns the tile that it's placed onto into a puddle of water that deals damage to enemies that step on it and can petrify them. Dries out after a while.

Milk: Similar to holy water but can be placed on occupied tiles. Increases the fire rate of babies standing on top of the milk puddle.

Lil'Delirium: Straight up imitater from pvz. Granted battery already exists but it can still find some use. Turns into a duplicate baby card.

Worm Friend: Works similar to Hungry Soul. Pops out of the ground and slows/immobilizes and damages a single target that stepped on it. Can be eaten while it's dealing damage.

Kicking Baby: Kicks cube babies at enemies. Lobbing them through the air and dealing splash cold damage. Essentially winter melon from pvz.

Wisp Baby: Surrounds itself with 4 wisps that orbit it and shoot at enemies. The wisps are fragile and can be easily destroyed by enemies or cold baby shots.

Lil' Necro: Mini version of the Necro enemies from isaac. Shoots magic bones from the front of the map to the back, similar to the abel ghost baby.

Host Baby: Defensive baby that'll open periodically to shoot. Is practically invulnerable when shut, even to explosions, but has very low health when open.

Godhead: Shoots a tear with a mobile aura effect, similar to the one suggested for Succubus. Very strong and expensive. 

That's all I could come up with on the fly, if even one of these make it in I'd be incredibly happy.

I love this game to death (this account was made JUST to leave suggestions to your game), meaning I have a lot of problems with it, because I want it to be perfect (impossible)

To make this easier to read i'm just going to post my two main ones, Boss battles are lame, the first 3-ish levels are boring.

For boss battles, It's kinda lame how I can't select babies, but dealing with recharge in a boss when they can just instant kill 3 lanes sounds bs, my proposal, make the bosses instant kill moves (plum gun, ragdoll skull, middle horn laser) only happen once or twice at specific health values (1/2 1/3, whatever) and/or make babies recharge and hearts fall both twice as fast in boss battles. You can even make this only apply in hard mode, that would make me play it a LOT more (personal preference, hard mode is fine.)

For the starting a run issue, it's already super fast so it's not a big issue, it's more of a personal thing. Maybe after beating hard mode, you can select from a starting deck, with a unique upside and downside to choose from for each one. Basically, after beating hard mode you unlock characters to choose from, and after winning a run (hard/normal/both, idk) with one of those characters you get an achievement with like, isaac baby, maggy baby, cain baby. Legit I would spend so much time playing a lost character that can't get heart producers, but babies and actives charge twice as fast. You could add the worst fucking thing imaginable, and I'd play the game for a month without giving up.

TL;DR, I would like to select babies before a boss battle, because random babies are kinda lame. Different ways to start a game by selecting prebuilt starting deck with some kind of drawback and upside would add a lot of replay value, especially if winning with a deck gave an unlock.

The D6 is currently meh. Most often you already find one of babies good enough, and even if both are so-so, there is a "?" variant. Plus later, on loops, when there are no more babies to select, D6 gets totally useless.
Propose another use: when clicking on dice(after each level obviously), player selects one of babies already obtained, and D6 replaces it with random baby that player doesn't have. This will make item potent in any stage of game, while still random, and interesting due to possibility of getting baby player missed earlier.