So imagine Plasma's goal was completely different - what else could've it been? And what OTHER than freeing Pokemon would've been effective? Maybe aim to combat extinction in the region? Be creative! And please don't say "only freeing Pokemon could've been done" 'cause your post will be irrelevant. This thread is about what other goal they could've had. ;)
I think that if Team Plasma's goal had been to make people fear what they were doing to the environment, and what that was doing to the pokemon, that could have worked. If they had been able to show the people of Unova how waste from Castelia was polluting the ocean/city, how more and more trubbish/garbodor were amassing near major cities, how Nimbasa's light pollution was affecting the natural world, how Driftveil's mining was destroying habitats, releasing dangerous chemicals and contributing to more pollution from the shipping, and how pokemon battles were expensive, requiring specific facilities dedicated to using a ton of electricity and resources to heal pokemon and then fix up gyms etc...
they might have just been able to control the region. Once people saw all this, team plasma could twist this good cause (of protecting the environment) and made people fear what they were doing. By showing these examples - and showing the possible future consequences, Plasma could have struck fear into the hearts of the masses. Soon enough this would have blown over as we humans are apt to forget instead of heeding the warnings given to us... and then Plasma would have staged a disaster. One of region-wide affecting proportions, this disaster which they'd say was based on climate change, would tear the Unova region apart, creating an apocalyptic Unova. But, out of the darkness, a hero would rise. A hero whose ideals/knowledge of the truth could unite Unova. Team Plasma's king and the hero of the entire region would be able to assume control over the region, and team plasma would have control along with him.
As for what kind of disaster do you say? They could use their trubbishes (and sandiles/scraggies with sludge bomb) to spurt poison into the rivers. Their trubbishes/scraggies/purrloins/patrats could create a region-wide drought if enough amassed in areas throughout the region and used sunny day. Similarly, these trubbishes/scraggies/purrloins/patrats could create floods with rain dance, with the patrats creating thunderstorms using thunder. (all could be blamed on us humans)
Maybe Team Plasma could've attempted to stop urbanization in the Pokemon world; they could be like an eco-terrorist group, fighting for the preservation of forests and fields that are the homes to Pokemon. Castelia City would obviously be a prime target for Team Plasma as they battled to save the homes of Pokemon and protect them from the negative effects of living near humans.
Considering "Freeing" Pokemon wasn't even their real goal, there isn't much to contribute. Team Plasma was attempting World Domination using sympathy to guard them from most attacks. Demonizing the sport of Pokemon Training and using pretty speeches to make them look as if they were sincere about what they did.
In reality they were a cross between Rocket and Galactic. They stole Pokemon from Trainers and abused wild Pokemon that held significant possible promise to their goal.
Some members of Plasma were seduced by Ghetsis' silk speech about freeing Pokemon while others were there for the real scheme behind the false advertising. Ghetsis wanted to Dominate if not create an entirely new Unova using N as a Poster Child to lead the way.
They covered many plot basis. Only thing that could have been different was if they were to really go PETA on the Trainers and not focus on World Domination but segregation of Pokemon and Humans.
Team plasma was just a bunch of hypocrites. They wanted to free pokemon, but what did they do? They used pokemon to battle.
Not only that, there's this whole genesect issue we are neglecting to mention. They want to free pokemon, but they are turning a Pokemon revived from a fossil into an artificial monster? Sounds like team plasma is evil to me.