The Three Most Popular Transformers

1. First one is the easy one: Optimus prime, the leader of the Autobots. The main reason is apart from being super cool Optimus prime he represents "good" vs "evil" and it's a given that most people have a soft spot for heroes..
.
.
.
.

2.
Second, I chose the the "little brother" of the heroic Autobot faction: BumbleBee.
Constantly trying to prove himself to the taller, stronger robots, he takes risks that put him in danger.

That's probably why people feel so attached to this character.
Once again most people like underdogs.

.
. Maybe it has something to do with the fact most people are underdogs in their own respective lives? 3. Third choice is also pretty obvious.
  I have to go with the primary antagonist and leader of the "evil" faction: Megatron.

As you probably know, Megatron is the leader of the Decepticons.
He's one mean robot, that's for sure! Although he is as powerful as Optimus Prime, he's much more aggressive and usually creates havoc where ever he goes..

.
So why choose him? Considering there wouldn't be a story worth following if there was no enemies it's a given but also because if you take the time to understand where "he comes from" you might realise he's also fighting for a cause. His cause.
So you have to respect that.

Isn't that like real life? There's always a good and a bad in any confrontation but if you look closely and objectively you'll find that these titles ( good and bad) change hands depending on the perspective.

.
. There are others like Ratchet, Ironhide, and Jazz who  landed on Earth and taken the forms of  vehicles too.

There are also Scorponok, Ratbat, Shockwave, and Bludgeon whom all led the Decepticons, overthrowing Megatron in the process or taking over the group during the time when Megatron was believed dead.