Honestly, the only times the plants lose in Herbal Assault are when they stay back and play TDM instead of pushing the objective.
Honestly, one of the biggest offenders against balance is Super Brainz, particularly Electro Brainz with his OP beam. He's supposed to be the Zombie equivalent to the Chomper, yet he has more hp (barring the Armor Chomper) and has a ranged option. I'd say a safe balance option would be to reduce his max hp by 25 to be more in line with the chompers - and obviously nerf electro brainz's beam. His spin already gets shut down by em peach, spin dash, burrow, or spikeweed. (only problem is pubs don't spam Citron or Chomper much to counter him)
The Citron is cruelly underestimated, especially when it comes to stopping spinning imps (and their mechs) or superheroes. The beam can get plenty of kills on the lower hp classes if you use the beam wisely - or drive them behind cover, letting you push. Frozen Citron actually does more damage per tick than the regular with added freezing at the cost of less beam duration. The ball mobility is great for mobility and pushing - and it's a hard thing to shoot at top speed.
The cacti are fine provided you don't get spawn camped by superheroes, all stars, or z mechs. Less pressure means more time to snipe your low hp zombie counterparts. Deadbeard only has two variants (Three if you count the party variant) that are worthwhile overall. And Zen Cactus is still plenty strong - dunno what you're on about.
Scientists get shut down by clever Chompers and Peashooters using hyper. If you eat a scientist, they're unreviveable, which means they cant revive/heal their team, and one less zombie to worry about for 10-20 seconds. If there's a cluster of scientists, go peashooter or corn. Hyper peas are hard to shoot, they can potentially stop reinforced pushes with bombs, and the splash damage adds up.