These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Complete Monster: Dr. Merrick is at first a charming and helpful doctor. He has the clones under his care dissected alive when he views the need as arising, and lies by telling them they'll be sent to the mysterious 'Island,' while lying to the clones' original source by claiming the clones are brain dead and are not living, sentient beings. When one clone's original donor is already dead, Merrick spitefully plans to have her harvested anyways, and attempts to kill any clone who resists him. Drunk on his own genius and power, Merrick seems to view himself as some sort of twisted messiah.
Crowning Music of Awesome: The music of the same name, composed by Steve Jablonsky. Listen as the tension and the emotion slowly builds up...and then suddenly explodes in a shower of pure, saturated epicness. Seriously, how did this music not get any awards?
Genius Bonus: Tom Lincoln's comment about how Six Echo was worth all the money he spent on him when discovering that they have the same finger prints can seem a bit Captain Obvious, unless you know that finger prints are not genetically determined. Not even identical twins have the same finger prints.
The woman who gave birth and smiled at her baby only to be killed seconds after the child is taken from her.
They Wasted a Perfectly Good Plot: The film sets up what could be an emotionally wrenching decision, namely asking whether it would be worth it for Jordan to sacrifice her life so as to prevent Sarah Jordan's family from losing a wife and mother. Unfortunately this is rendered completely moot by the revelation that during her accident, Sarah Jordan suffered massive brain injuries from which she had absolutely no hope of recovering.
And isn't it convenient that they avoid any (more) possible moral dilemmas by making the real Tom Lincoln an absolute douchebag, even though as The Onion pointed out the clones do a whole load of damage and endanger - and possibly END - lots of innocent original people's lives?