Natural selection doesn't favor traits that are somehow inherently superior. Instead, it favors traits that are beneficial (that is, help an organism survive and reproduce more effectively than its peers) in a specific environment. Traits that are helpful in one environment might actually be harmful in another.
(one again, I hope this helps ^^)
It is possible for large molecules to enter a cell by a process called endocytosis, where a small piece of the cell membrane wraps around the particle and is brought into the cell. If the particle is solid, endocytosis is also called phagocytosis.
