It's actually not all that difficult if you put some thought into it. Here are some suggestions I came up with:
*No "Eco-Villains." Instead, have the Planeteers respond to problems resulting from ecologically unsafe practices. Ideas include pollution-spawned mutant monsters (like the movie Prophecy with the deformed psychotic bear spawned by mercury pollution), killer mudslides caused by deforestation, loose Soviet nukes, etc. Maybe there's an antibiotic-resistant plague resulting from excessive use of antibiotics in agriculture and the Planeteers have to bring in the one effective drug and fight a bunch of criminals trying to steal it and sell it? I remember one episode features a panic about a shark leading to mass killing of sharks and a resulting plague of jellyfish, so it's not like the idea wasn't there.
*Subtler, less ridiculous portrayals of polluters. Nobody seriously wants to destroy the environment, regardless of what the show depicted. According to one of my writing books, the "polluter" character in The China Syndrome is not a bad guy--he cuts corners to cut costs to create more jobs. One CP episode featured an Indian prince who allowed a forest to be cut down to build a resort to generate jobs for his people--since this was something they did in real life, it's not like they weren't capable of subtlety.
*If there absolutely must be Eco-Villains, dial them down a notch. I had the idea for a pollution-spawned mutant messiah who thinks his kind are the next stage of evolution and wants to rule the world. It turns out there actually was such a character--Verminous Scum. Obviously he'd have a more subtle name--I suggested "Lord Vermin" as a name he gives himself to scare people. Alternatively, just buy the rights to the Skaven from Games Workshop's Warhammer Fantasy--they're not as well-known a fantasy race as Orcs, Dwarves, Elves, etc. so they'd be new and innovative. They can be depicted as a dangerous race of mutants, with some moral grayness courtesy of "good" Skaven who want to share the Earth with humans and murderous racist humans who want to kill all Skaven no matter how peaceful (some of) them are. Another idea could be to have the Planeteers prevent a bin Laden-type figure from getting his hands on unattended Soviet nuclear weapons and he swears revenge, becoming a recurring foe. A PC-type like Ted Turner isn't going to go for that, but he could still be an interesting enemy.
*Don't make Wheeler (the American character) a hothead dumbass. Seriously, do you think Americans are going to want to watch a TV series depicting them so poorly?
*More focus on non-Western environmental pollution. There was one episode where the Russian girl went home to find her hometown getting wrecked by a slipshod Soviet-era mine or something. Depict how environmentally-destructive Communist regimes have historically been. Dedicate a whole episode to the draining of the Aral Sea, for example. The "loose nukes" episode could have Linka pontificating about how horrible life under Communism was in order to put some Western environmentalist who's green on the outside and red on the inside in their place, with the Soviet regime's nuclear weapons now getting bought up by terrorists and malevolent dictators.
Here's a suggestion the board member whose handle is Admiral Hook came up with:
*Captain Planet is actually some kind of being summoned from a ecologically-devastated future back into the past to change history. When he's in the present-day, his body in the future is comatose, which could present some real problems Indian in the Cupboard-style (IIRC a WWI soldier brought into the present-day as a figurine was killed while asleep in a trench due to being summoned). If there's a parallel future storyline (perhaps involving a war on the blighted future Earth), that could be a way to build up some suspense.