Rank the Villains!

If I ranked my favorite teams it would go

1. Team Galactic
2. Team Plasma
3. Team Rocket
4. Team Aqua
5. Team Magma
6. Team Flare

My reasonings are similar to your though I think Rocket had a lot more going for it with the interesting story of Mew and Giovonni. Also Plasma made such an interesting argument to how Pokémon should be used and though the generation wasn't my favorite, the villains saved the game for me. Team Magma in my opinion wasn't as detailed and focused as Team Aqua, though they rank almost identically since they were meant to be super similar. Team Flare could have been cool but they were just too much, and too little, nothing sat right with them. I also have not ranked Team Skull as I need to see them in action more then a demo before I can completely decide if I like them or not.

 

Oh boy, this is going to be really hard, but I am going to try.

1. Team Plasma - Somehow they made me think about what we are doing as trainers in Pokémon. Now I don't agree with them at all, but they had a small point. And they believed in their cause. Truly believed. It was not just shits and giggles for them. Their faith was strong until the end even if they went about it the wrong way. Neo Team Plasma were ruthless jerks with less honorable intentions than the old, but it made for such a good contrast between the old and new.

2. Team Rocket - Ah, the old, the original. I still am not sure about what was their precise purpose, but they had a fearsome purpose. I was actually terrified when playing through the Rocket parts in the past, not to mention how much of a pain the spinning tiles were. I tell you that was their most evil thing. And Giovanni is the boss.

3. Team Magma - I have to agree with @[member="TheBlazingInfernape"], Maxie is one badass boss, to keep it PG. They are high up on the list because I can appreciate them not stumbling around like drunken sailors. They operate in a way more business-like way than Team Aqua. I always play either Emerald or Alpha Sapphire and it is always Maxie that I appreciate more. If I had to choose I would rather have a cold, calculating, grounded Maxie leading my team.

4. Team Aqua - The different personalities from Team Aqua clash together nicely. They complement each other. Shelly's shrewdness, Archie's Passion, and Matt's loyalty, they are things I would admire if they weren't the bad guys. I just don't like the fact they seem so disorganized to me.

5. Team Galactic - Their characters lacked a certain depth to me. While they were a good Team and actually came really close to their goals they aren't on the bottom of my list. But really being so openly bad is just bad for the business.

6. Team Flare - Idiots in red suits. They had the least compelling story and the least believable cause. Just beautiful people surviving? They are not even that good looking, Dorito man.

I will have to wait until S/M is released before I judge Team Skull, but so far I am not impressed. I am still on the edge about them, seeing as they look more like harmless thugs.

 

1. TEAM AQUA I love them so much and Archie is so good and pure? I love it
2. Team Plasma I could actually see where they were coming from originally, since there is a lot of cases in the anime at least of bad trainers caughpaulcough
3. Team Magma Maxie has a well organized team here and increasing the landmass would actually help a lot ^^
4. Team Galactic Their goal is meh but I love the commanders
5. Team Rocket Same as Galatic, but I like Cyrus more than Giovanni
6. Flare, Lysandre is beef but the rest are like, bland

 

My rankings are as follows:
1) Team Aqua/Magma: I love Archie and Maxie and they think they're so cool in their outfits when they're not and climate change about the land and the sea's balance~
2) Team Plasma: Mad intense and the whole N backstory kinda got me in the feels.
3) Team Flare: They were wayyy more intense than team plasma, but it was so obvious that Lysandre was the villain, but I loved the aftermath after team-flare was disbanded.
4) Team Galactic: I liked their outfits, but I never really liked their ideals in capturing the lake trio. I played Pokémon Platinum, and I liked the ending there, but not in Pearl/Diamond.
5) Team Rocket: Honestly, imo they were just in just because, and I wasn't a fan of their outfits.
6) Team Skull (Or Aether Foundation): Mainly Because I don't know much about them yet,

 

(from the games i've played)

team galactic
team rocket
team skull
team aqua
team magma
team flare

galactic had the greatest ambitions of all the villains, or least I think they did

 

Some of this was rather difficult as there are some things I like about some teams, things I really don't like about others... All the same, there was something I liked about all of them and here they all are (warning, lots of writing ahead!):

Team Skull - Oh my. First of all: they weren't the true bad guys. That was a refreshing change. On top of that, I found them a great deconstruction of what happens to all the kids who dreamed of being a great trainer, only to have their dreams crushed by those stronger than them. Something like losing too many Gym matches or failing the Trials is bound to have a significant impact on a ten year-old's self esteem and here you have what they've become. They don't want to destroy the world or liberate Pokémon or savagely murder everybody, they just want enough money to survive. This gave them a much more realistic and human feel than the other teams. On top of that, Plumeria is a perfect admin, I found Guzma both sympathetic yet a compelling antagonist and I found myself snickering every time the grunts came onscreen. (Also, their boss trained bug types. Who could have seen that coming?)
Team Aqua - The moment Archie appeared in my playthrough of Alpha Sapphire, I knew I was going to love this guy. I loved the casual feel his grunts seemed to carry about them and the fact that he always seemed to be in a good mood. I actually looked forward to running into him or the rest of his team, which usually isn't something that people do in regards to evil organisations.
Team Plasma - Loved the cause these guys stood for, it was rather confronting to have these guys popping up while trying to fill in my Pokédex. Ghetsis's role as a master manipulator was rather interesting. However, my main issue with this team is that all of that dissolved toward the end of the game and it was revealed that their big plan was to take over the world. I have to say, I was pretty disappointed that they had to get rid of all the grey morality at that point, especially since they'd done so well at stopping everything from being too black and white. All the same, the characters of N and Ghetsis and the toxic relationship between them was pretty well done and I liked seeing N evolve as a person.
Team Galactic - Probably the most ambitions Team we're ever going to get and I applaud them for almost succeeding. It's been a while since I've played the Gen 4 games, but I remember that moment in Mt Coronet when Palkia was creating that new world and I thought "Oh geez, he's going to do it. He's done it.". I found Cyrus an interesting antagonist and honestly, the more I think about him and his team, the more concerned I get. They're all practically a massive cult worshipping a man capable of destroying worlds... Brr!
Team Rocket - Team Rocket doesn't have much in the way of motive, but they make up for it in ruthlessness (killing Cubone's mother? Hello???) and the nostalgia of being the first team you beat into the dirt. Over time, I've been finding Giovanni less intimidating, mostly because you can sweep his entire team with a single water type. They were once a truly intimidating (though at times, slightly goofy) gang, but I feel that a lot of that was tarnished by the anime's version's glaring incompetence. All the same, I can't bear to but them any lower on this list.
Team Magma - I loved Maxie's redesign in ORAS. In fact, I loved everybody's redesign. Tabitha, Courtney, the grunts... On top of that, the remake exaggerated their differences with Team Aqua, making their rivalry all the more better. Their motives are a little too similar to Aqua's, but I can ignore that. Also the animation that plays when you beat Maxie will never not be entertaining. The only reason why this is so low on the list isn't because I dislike Team Magma, I just like so many others slightly more.
Team Flare - Despite everything, i don't really hate Team Flare that much. I feel they had a lot of potential that was completely wasted. They made a team that was willing to wipe out most of the world. An ambition almost on par with that of Team Galactic. The worst thing they did was make all the grunts act like total buffoons. That made sense with Team Skull, where they're a bunch of kids that don't know any better but come on, these guys are willing to leave complete lasting damage on the planet. A tiny bit of backstory on the team and Lysandre wouldn't have hurt, either. Overall, I think Team Flare was actually a really good idea, it was just poorly handled.

 

My rankings don't all have very detailed reasons XD haha but...

1. Skull: beacuse no team has been so awesome just from the very first minute as these guys omg, the designs and the hilarious walks/dances etc, it's just so great, very refreshing from the others before them and so fun. Great grunt design which is a must for these teams because you end up having to encounter so many of them. My face literally lit up when I saw the first grunt it was amazing.

2. Rocket: because classics are always high on my list, I don't love them in the anime but I dislike the anime in general anyway, but seeing them feature in the games, awesome. They also have a great grunt design.

3. Magma/Aqua: because that was the next most memorable to me in terms of plot, it was a unique new motivation for them on a grand scale and worked in well with the overall story and region, plus Mama has a great grunt design (aqua less so)

4. Plasma: a little on the forgettable side for me at this point but I liked the idea of N and his relationship to the rest of the team, the concept of not wanting Pokémon captured is like addressing the elephant in the room (we enslave wild animals! LOL)

5. Galactic: I don't really remember it much, maybe the design a bit? haha

6. Flare: Again I don't even remember them much but I can remember finding them annoying in terms of design so that makes them last.