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Who is the better and more effective unit on the table top for its points motarion or Magnus?

depends on what else you're running and how you support it.

When both are taken in a list, usually you try to kill Magnus, then Morty, but it all depends on what else is there.

Mortarion probably. Primarchs are less common now than previously but I feel like I got the sense you remove Maggy from your list before Morty. Mortarion is quite a bit harder to kill T1 without buffs.

Mortarion does nothing until he gets within charge range. Unless you cast warptime on him, he often takes up until turn 3 to start smashing things, because the enemy can just withdraw from him. Once he gets into combat, anything he touches withers and dies, but he won't be making back his points by smashing guardsmen.
Meanwhile Magnus is faster (16" instead of 10") can cast buffs and deal damage starting T1, cast warptime on himself and be anywhere he wishes to be. He will remove a unit from your army every turn until killed.

However, if you assume they get blown off the board T1 (which happens about half the time in my experience), Mortarion is significantly more durable due to disgustingly resilient, which also protects him from mortal wounds.
In addition, Magnus suffers from not actually doing anything unique for his army, since Ahriman and his DP council can pretty much do everything that Magnus can do, but enjoy character protection.