Cats and dogs are similar, but different. A stagecoach and a Lamborghini are very similar. They share the basic fundamentals. Does that mean they evolved from each other? Why is the chromosomes of animals are in conflict with the evolutionary line. Ferns have more chromosomes than humans. Are ferns more evolved than humans? Tobacco has more chromosomes than humans also. Does that mean that they are more evolved? I think that's why people smoke. They want to become more evolved 
There is no "more evolved". Evolution isnt a ladder. The number of chromosomes only determines that, the number of chromosomes. It has nothing to do with "perfection". Down's sindrome is caused by an excess of cromosomes, for example. Trully, a godly design, a reproduction mechanism so flawed that wastes an entire pregnancy in an animal that will starve to death due to brain damage caused by incorrect reproduction of DNA.
1. My point is if evolution is true then we should see the chromosomes more aligned with the evolutionary tree which we don't.
Who predicts that? Why? Chromosomal evidence is used to show relationship between species, and as Rama Set pointed out, the fusing and duplication of chromosomes was a prediction of modern evolutionary theory that was then confirmed.
2. We are looking at a copy of thousands of copies even if you believe in YEC. Things can and will break down after all that copying. Would you look at a wrecked corvette and ask Chevy why did they built it like that?
So you are saying that animals DO change? Because that's all you need for evolution. A faulty copy mechanism. Besides, believe it or not, there is no reason to believe the copying was any better in the past. Why would it? We have a similar replication mechanism.
And, no. No one is saying cats come from dogs or viceversa. Cats and dogs are distant cousins. They can both trace their origins back to an animal. Cats and dogs share an order, Carnivora, and one being part of the sub-order (?) Feliformia, and the other of the Caniformia. Their exact most recent ancestor isnt known, as far as I know, but it is now thought that they share at least an ancestor in the members of the Miacids/Miacedae, as all Carnivora do.
Just because they're carnivores now doesn't mean they were always carnivores. Little tike was a lion that REFUSED to eat meat. They used him in movies. But changing from a meat eating lion to a plant eating or vice versa is a small step compared to getting a lion from a rock.
Dude, the name has nothing to do with whether they are carnivores or not. Pandas are strictly herbivore and they are part of the Carnivora order. And most animals I know of that are in the Carnivora order are either not strictly carnivore, or out right omnivore.
And no one is saying you got a lion from a rock. What we are saying, in a terribly simplification of millions and millions and millions of years of both geological and biological history is that a feline like animal is the ancestor of cats, and that a small horse-like animal is the ancestor to horses. But that horse-like animal had an ancestor. Eventually, as DNA evidence, fossil evidence, chromosomic evidence, mitochondrial evidence (mitochondrias, by the way, used to be individual cells, and now cohexist in symbiosis with most eukariotes.It even has its own DNA, and we can trace it back just as we trace any other DNA source. Even better, at least in humans, mitochondrial DNA is transmitted via maternal line, meaning mixing of genomes doesnt occur, allowing for extremelly precise dating), quirality evidence, continuous function evidence, and much more tells us, its obvious that ALL living beings we know of share a common ancestor. Where did this ancestor come from is a different issue, but abiogenesis shows us some mechanisms that may have allowed for proto-protolife to emmerge.