I don't understand how Palpatine couldn't sense Luke's presence on Endor when Vader could. Granted, Vader was Luke's father and had more of a bond, but why not Palpatine?
As you said, Vader had more of a bond than Palpatine. Not only was Vader Luke's father, but he had also personally encountered him several times, sensing the Force in him during the Death Star trench run and also dueling with him at Cloud City.
Palpatine, on the other hand, had never met or encountered Luke.
The Emperor himself theorizes that it was due to their familial connection/paternal emotions:
Darth Vader: My son is with them.
The Emperor: Are you sure?
Darth Vader: I have felt him, my master.
The Emperor: Strange that I have not. I wonder if your feelings on this matter are clear, Lord Vader.
Darth Vader: They are clear, my master.
Despite Han Solo's admonition to Chewie to "Keep your distance", the shuttle was VERY VERY near the Super Star Destroyer that Vader was on - almost on top of the SSD bridge when Vader sensed Luke; and far from the Death Star.
It's quite possible that the Emperor was simply misleading Vader when he said "Strange that I have not". He himself, in the same conversation (As well as a previous one, before sending Vader to command ship) notes that he has foreseen this:
Vader: What of the reports of the rebel fleet massing near Sullust?
The Emperor: It is of no concern. Soon the rebellion will be crushed and young Skywalker will be one of us.
Darth Vader: He will come to me?
The Emperor: I have foreseen it. His compassion for you will be his undoing. He will come to you and then you will bring him before me.
The Emperor did sense Luke.
From the script, The Emperor knows that a small rebel force has landed on endor, as he says that " Yes I Know" in no surprise. And when he questions Vader that if he(Vader) is sure that Luke is on Endor, Palaptine was very cool.
69 INT EMPEROR'S TOWER - THRONE ROOM
EMPEROR: I told you to remain on the command ship.
VADER: A small Rebel force has penetrated the shield and landed on Endor.
EMPEROR: (no surprise) Yes, I know.
VADER: (after a beat) My son is with them.
EMPEROR: (very cool) Are you sure?
VADER: I have felt him, my Master.
EMPEROR: Strange, that I have not. I wonder if your feelings on this matter are clear, Lord Vader.
Vader knows what is being asked.
VADER: They are clear, my Master.
EMPEROR: Then you must go to the Sanctuary Moon and wait for them.
VADER: (skeptical) He will come to me?
EMPEROR: I have foreseen it. His compassion for you will be his undoing. He will come to you and then you will bring him before me.
In other words, he is misleading and double-crossing Vader at this point.
This is supported in a QnA session:
Question: Why couldn't the Emperor sense the presence of Luke Skywalker on Endor (per his conversation with Vader)?
Answer: The Emperor did sense Luke. He just didn't tell Vader that, because he was planning on replacing Vader with Luke (kind of like replacing an old sedan with a new sportscar) and double crossing Vader.
I think it was probably just Palpatine's habit to keep Vader guessing. First he claims not to have sensed Luke then he claims to have foreseen Luke being brought to the Death Star. This practice leaves Vader unsure of just what Palpatine is and isn't aware of. It forces Vader to consider his scheming carefully because his Master may be aware, but doesn't stop him (you want your Apprentice to scheme against you to keep you both sharp). In short we'll never know, but I suspect Vader's feelings on the matter gave him extra sensitivity where Luke was concerned (and set off warning bells for Palp).
Palpatine sensed a disturbance in The Force in Empire Strikes Back, and identified its source at the time, but by 1983 George Lucas was more concerned with merchandise sales than gaping plot holes.