There are too many changes with Evolution for this to be canon with literally NO explanations... So I feel I should drop a few theories.
The Towers.[]
The Towers in Evolution were the towers used all along, and the towers in the original Code Lyoko (the visual we saw) was an outer shell for what is now the Evolution Towers. The outershell to which was lost in data corruption. Explaning why, when the tower was hit in the original Code Lyoko, it shook, and moved like it was gelatenous, but when the tower is hit now, it stays stationary.
The New Supercomputer.[]
Sometime between Echoes and XANA 2.0, the factory was discovered by a business owner, who decided to use this as an opportunity for business. Simply, by luck, he made it to the supercomputer. He deemed it old and unsatisfying, and decided to put all the software onto a newer CPU. When having wasted money on it, when it has a bunch of locks and codes, and stuff he couldn't dream to understand, he goes back to and sticks to the upper floors, eventually giving up on the factory for it being too rundown, and him being in too far of a whole for all the money that he put in it.
The New Sewers[]
Because of a rat problem, the city got some cement, and paved the inside of the sewer. They also drained out all the water (though that was self explanitory) And to make SURE no rats could escape, the raised the manhole, and made it more complicated to get in. Their boards and scooters...well...got lost in the clutter of their rooms or something
Samantha Suarez[]
Unfortunatley, and I know this is gonna piss alot of people off...SAMANTHA SUAREZ AND SAMANTHA KNIGHT ARE TWO ENTIRLEY DIFFERENT PEOPLE. Odd's attachment to the new Sam, well, lemme explain. Something happened to Samantha Knight (death possibly), and Odd chased after the next best. Someone with the same name and back story. Her attitude towards him stems from well, the fact that she knew him for more or less a year.
Odd's hair[]
Bad haircut
Ulrich's Random Height change[]
Puberty's a b*tch
Changes in their rooms.[]
Someone decided to decorate. Duh.
Anything else left unexplained, leave in the comment section below.