If you could make an option to turn off the flashes after explosions that would be great, on The Ark my head gets all fuzzy because of them.

The Binding of Isaac fangame, heavily inspired by Plants vs. Zombies · By
I think there should be a sure-fire way to counter the babyplum-incarnates. If you have a full defense, they just fly right over it, and there's nothing you can do about it. Also, add trinkets, that would be cool. Like, cancer could slightly increase all tower's speed, or curved horn could make babies do slightly more damage, things like that.
Replaying the first level(s) is kinda repetitive due to always starting with the same units therefore just using the same strategy over and over again because at this point the enemies pose no challenge. To solve this you could possibly add some randomness to your starter deck (let bobs brain be a random unit for example), or as alternative you could add some different enemies that force using a different strategy early on (although this might not be preferable due to information-overloading new players). One last possibility might be some sort of 'challenge/reward', where before the level the player can take on a challenge (e.g. only use 18 spaces). If succesfull they get a reward (e.g. coins or an item) and if they fail maybe some sort of penalty. This would at least force some kind of variation on the first couple levels.
The game has a great concept, I'm looking forward to see how it'll progress!
Since 2 of the most common complaints are "need at least one more seed slot" and "no way to deal with lobber-specific enemies if you weren't offered a lobber tower" we can kill 2 birds with one stone:
Add Sister Maggy as a 5th starting tower. She has the same damage and cost as Brother Bobby, but shoots in an arc. There, 2 problems solved!
I was stupid/drunk/inattentive enough to start a new game instead of continuing my first playthrough. Or maybe it has ended because I died on the second boss fight, I dunno. Anyway, if it's my fault, can you please add a warning message saying something like "You're about to start a new game, your previous progress will be reset." Thanks!
I would suggest on the boss fights to be able to place the babies immediately after clicking on them without having to snap to the hot bar to then place them on the map. This takes a while and leads to unavoidably losing a charger. (Lost on the last hit to the third boss due to having to wait for the hotbar to place the baby on a spliting fly)
Not sure if they're already in the game or not, but it would be cool to have blue flies in the game. Maybe when a Mulligan's mask is broken, if you manage to kill it before it escapes it can produce three blue flies. They'd home-in on an enemy and hit it once, killing the fly in the process just like in Isaac.
I also agree that the number of slots for babies would be nice. I've got so many babies, but C.H.A.D. and cube of meat are almost completely necessary.
Any enemies completely immune to one of more damage type. I'm looking at you red fly and weird host hat thing...
I haven't gotten past mines, so if there's more I wouldn't know.
As for what to do about these enemies.
Red Fly should get tired after flying over a single tower or two, giving a brief window that the towers behind can hit him a couple of times.
And Host Hat... thing should have the hat as an armor rather then a lobbing damage immunity, IMO.
Especially since these two enemies appear on the same levels and are immune against what the other is weak against.