The system "prefers" Evan because Evan skates to the system. However, he was extremely lucky to win the gold medal in Vancouver. The other guys didn't bring their best (Though Dai came close, he just shouldn't have gone for the quad.) either performance or technical. Johnny did, but he doesn't go for teh highest number of points even starting out on paper
The judges are to blame for that, though. Again...the sport is supposed to be 50% technical and 50% presentation. People shouldn't be rewarded for "transitions" just because they put extra movements before and after jumps. The guide for scoring jumps already includes a bonus for transitional movements. That program component should possibly be done away with altogether since the transitions of a program are covered under CHOREOGRAPHY and how well the transitions are executed is covered under the PERFORMANCE and SKATING SKILLS scores. Either that or jumps should not get bonus GOE for transitions unless it is an especially difficult transitions. The GOE guidlines for scoring jumps are actually pretty bad at the moment - only a single bullet point addresses both the height and length of a jump...which is what's often most important in a JUMP in the first place!
Since the Transitions score is in fact a mark the judges have to evaluate right now, though, it should be especially about how well a program flows and the uniqueness of transitions. Which are both actually taken into account under the scoring guidelines, seeing as these are the 4 listed criteria for judging Transitions - "variety, difficulty, intricacy, and QUALITY".
Here is a very important note, though - Doing extra movements in and out of jumps isn't necessarily a great transition. The judges don't seem to understand this. Strong and smooth skating edges in and out of a jump, and continuous movement after a jump has been completely, should be considered a perfectly fine transition.
The "Interpretation" mark is really where the judges have not done well. If a skater is including transitional movements solely to boost that score and the transitions don't benefit the music, THEIR INTERPRETATION SCORE SHOULD DROP. I've never once seen a case where a skater's Interpretation score was lower than their Transitions mark, though. That's just bad judging.
A program by Evan Lysacek should receive a good-ish Transitions score if you want to recognize all the extraneous movements he does but only a program by someone like Jeffrey Buttle or Matt Savoie or Jeremy Abbott should have superior marks for both Transitions and Interpretation. Very few skaters actually incorporate "transitional" movements into their programs that are there because the music dictates it and even fewer do truly unique and difficult transitions. Matt Savoie's score for Transitions at the 2006 Olympics - 7.00. Evan Lysacek's score for Transitions at the 2010 Olympics - 7.95.
Now that's a joke if I've ever seen one. I'm not even going to compare their Interpretation marks because I don't feel like vomiting at the moment.
In the case of Johnny at 2010 Olympics it's fair to say his Transitions score should have been lower, but he absolutely should have been scored higher than Lysacek for Performance and Interpretation. The judges didn't follow through on that, however.
Really, only people with an encyclopedic knowledge of skating (and who are also good at math) should be accepted as judges. You'll find that most of the people sitting on panels do not fit such a description.