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The backstory makes it out to be a more or less life-defining decision which faction, Enlightened or Resistance, you select.
As far as I can see though, there doesn't seem to be any real difference, except for color, between the teams. Is there any difference at all, and if not, do we have any kind of hints, or maybe educated speculation, on whether that might be planned in the future?
Or can I just flip a coin?
There isn't any difference, and there isn't any indication of this choice ever having an effect, gameplay-wise.
The only difference between the two teams is that The Resistance seems to be more popular, and will probably remain so in the foreseeable future. So if you desire a more challenging gameplay, pick the Enlightened.
Resistance as loners is not true in my area. The personality of the faction varies between regional areas (even varies between areas of cities). There is no difference in gameplay (both factions capture portals and try to link them to create fields). The only difference is in the storyline of the game (which you can ignore if you want). In the beginning, the Resistance was against alien influence of Earth's society. The Enlightened side with the Shapers who have influenced human society with the use of XM. The Resistance try to stop this influence. More recent story elements have added a second a second alien race the N'Zeer. The Resistance hopes to tap the N'Zeer's use of AI to continue their resistance against the Shapers. The Shapers were against the use of AI, so the Enlightened now also work to thwart the influence of N'Zeer AI. According this storyline, both the N'Zeer and The Shapers have influenced humanity. I guess the Resistance feels that AI is easier to control than XM influence; while the Enlightened fear that AI poses a Terminator type threat. Essentially, Niantic (makers of Ingress) have tried to make the storyline balanced so that both sides can be right/good guys and both sides can be wrong/bad guys. So really, I would suggest you choose your faction based on who you want to play with. Go to a big public park (it is probably a portal farm), find someone playing who you like (probably walking laps around the park staring at their phone the whole time), and join their side :)
Meta and gameplay wise no, story wise it's basically " do you want to help advance humanity through accepting alien help or by turning us all into robots"
As far as gameplay is concerned, there is no difference at all between the two teams. As far as the players go, there is a subtle difference in the kind of people who are attracted to either side.
Resistance seem to prefer to be loners. They work as individuals, but seem to have greater numbers, so it balances out.
The enlightened tend to be more social and work more as a team and talk more, which due to the way the game is set up, balances out the fact that there are less of them.
Unless you are set on one team or the other, my advice would be to try and find out which team dominates in your area, then join the opposing team. This way you will be able to level up quicker, and hopefully balance things out a bit in your area.
The only difference is in the backstory, as well as perhaps on-the-ground regional differences. However, when people actually read the backstory before deciding, it does tend to show up in the teams.
Aside from the "social" vs. "independant" difference mentioned earlier, there was (at least early on) a decided device skewing on the teams. iPhone people tended towards "Enlightened" while Androids went for "Resistance".
Not really important, but kind of interesting.
Personality wise, each faction sort of has their own strategy. The Enlightened don't do that much attacking unless absolutely necessary and easily feasible, preferring to claim neutral portals, unless they're working as a team. Meanwhile, the Resistance just tend to grab everything they can possibly get, no matter what.
