Will I be at a disadvantage for picking a less popular team?

Solution 1:

On average, there is a slight disadvantage to picking the weaker team, but not one that will completely affect your game.

For most of the game, your team affiliation will either not affect you (spawn/catch rates). There used to be rumors about giving you a perk for that team, but there's been no real evidence since. (Even after the game was reversed engineer to see more of the "gears", like how many steps to make a spawn call.)

The disadvantage comes from the lack of opportunity to earn the Defender's Bonus that Gym Leaders get for having a Pokemon at Gym. If you join a team that is the weakest in your region, then you and your team will have issues in holding onto Gyms. (whereas the teams with more members can statistically attack, take over, and fortify easier.)

The biggest takeaway though is that this is only an opportunity cost. The weaker team might be stronger a mile away, the stronger team might not frequent the area you are as much. The number of variables are unlimited as to that the weakest team might control all the Gyms of a city since their members are organized. There's no hard-set disadvantage, just a fluid difficulty curve.

Solution 2:

The main effect of being in a less popular team is the ability to hold multiple gyms at the same time, and that way gain the daily bonus from holding a gym (10 gold and 500 dust pr gym).

Unless you can out level all in your area and dominate the gyms that way, you will be at somewhat of a disadvantage.

If the other teams out weighs you significantly they will most likely take over your gyms before you can control multiple gyms.

That being said, if your team has no competition in the area you might run in to the problem of gyms reach max level without you getting any Pokemon in them, and with no competition they will never be cleared out making room for you.

As a normal player you will most likely not see much of a difference there.

What is more important is how dedicated the players in your area are, if you have dedicated people on your team bring people together for events it can make a huge difference for your team in your area. That being said the more people the better chance of having people who take an active rolle in the community around the game.