Well, a simple answer to this is the definition of Genjutsu.
Genjutsu are techniques which alter the targets chakra flow, disturbing his senses to produce and make him experience illusions. These illusions may be almost anything that his 5 senses can perceive. Simply put, you can make your opponent taste, hear, smell, feel or see anything by altering his chakra flow.
Byakugan and Sharingan and Rinnegan, as dojuutsu they are still, however, just a sense. In this case, Sight. They are still fitted within the normal "Sight Sense", thus you can make a dojutsu user see an illusion. So yes, Sharingan, MS, EMS, Rinnegan and Byakugan user will all be put under a genjutsu and will experience the illusion.
The thing is that Sharingan, as it gets stronger, gains the ability to see beyond low rank visual illusions. This means that (according to our RP), 3T and above can see through B-Rank and lower visual genjutsu (genjutsu that makes you SEE something). However, this is associated with the Sharingan's augmented perception. This high perception is what pierces through the illusion and enables the sharingan user to see that what he's seeing is fake. Its not his ability to see chakra that makes it so even if people want to believe so. Simply put, the sharingan's analytical and perception abilities can see through tricks. But this is relating to visual illusions, not all illusions. A 3T Sharingan user will still experience pain from a B-Rank genjutsu. He will still be put under it and will have to release from it like all other ninjas.
"Abilities of the Sharingan:
-See through the chakra flow. The Sharingan can tell if a person is under a genjutsu because the person's chakra flow would be irregular.
-Incredible clarity of perception, allowing them to easily recognize genjutsu and different forms of chakra
-Ability to memorize any technique that he or she witnesses, apart from other KG techniques. The user can memorize ninjutsu, genjutsu, and taijutsu with perfect accuracy, allowing the user to use the techniques as his own."
And reguarding to the 3T abilities:
"Description: This is type of Sharingan has 3 tomoe. It allows the user to perceive motions, copy the motions perceived, and predict motions. An example of this is during the fight between Sasuke and Naruto at the Valley of the End. Sasuke could perceive Naruto's motions, copy them, and than predict what Naruto was going to do next. Essentially, to Sasuke through use of his Sharingan, it looked like Naruto was going in slow motion. When active the user now has the ability to keep up with extremely high speeds and mimic taijutsu exactly. With this the user can now copy handseals done by an opponent, and use jutsus as they do. The user must however be able to mimic the techniques, for if they are not physically able to preform the copied techniques they cannot do them. The user can now pierce through visual B rank genjutsu and below. Unlike the previous two sharingan stages this level has the ability to hypnotize a target. If however the target is too strong the hypnotizing with be ineffective. This can only be done on targets one rank below the use"
Byakugan users don't have an augmented clarity of perception but they do have an augmented vision. But it is vision non the less and it can be tricked as any other sense with a genjutsu. I think however, that low rank genjutsu won't work because in terms of enhanced senses, Byakugan represents the most powerful eye sight. So it should provide a resistance of sorts to visual illusions. The same with some other enhanced senses and genjutsu that affect that sense.
The thing is that, for example, if i make an illusion were i make the opponent see himself suddenly teleported into a beach with an infinite ocean nearby, if the illusion is strong enough, Byakugan users, even if they use the telescopic and X-Ray abilities will still see nothing wrong, as their eyesight has fallen under the illusion the same so all aspects that i produce on the illusion are intended to trick their eye sight... If strong enough, it could even make the byakugan user see his chakra flow unaltered. Its vision. Its a sense. Thus i can fall under an illusion. The same with all other senses.
Perhaps the difficulty is seeing or determining what level of resistance to a genjutsu does a Byakugan and Rinnegan user have.
Now as for directed eye contact, i agree with lili and keotsu. Direct Eye contact is pupil to pupil. And that means that even a byakugan user that wants to use a genjutsu that requires eye contact, must gaze directly, pupil to pupil with his target.
My two cents at least...^^
