The biggest problem I have with the game, by far, is the default limit of 4 babies.
Lil Chad, being the equivalent of Sunflower, is a must-pick for normal runs, so that leaves three slots open. I've almost always used Cube of Meat for the second slot, because the defense is very helpful against clumps of enemies, and it hard-counters the worm monster in It's All Mine. That gives me a mere two empty slots, and I have to use at least one of these for an offensive baby. Even then, I've found Brother Bobby to be reliable enough that I keep using him for the earlygame levels.
Thus, the strategy feels stale; there is little room to make creative loadouts with the babies I choose throughout the run. I've learned that choices matter much more for the bosses, because I think they utilize all the babies I've collected. For the regular levels, however, I tend to ignore most of the babies I get, because I constrain myself to a loadout that I think will work for the rest of the run.
Personally, I would set the default limit to 6 babies; that is the amount of seed slots which the original Plants vs Zombies starts the player off with. But I think even 5 babies would seriously open up the game.