Emerson's critique of the "mere thinker" is that rather than think for himself, he simply limits his ideas to those he's read in books.
To be sure, Emerson is not arguing that the American scholar shouldn't read books; he's simply saying that book learning should be combined with a study of nature and active work. In this way, the scholar will learn that he is part of a vast cosmos in which everyone and everything is connected.
However, so long as scholars confine themselves to book learning and nothing else, then they will be unable to develop as either individuals or intellectuals. Emerson prizes originality and individuality, and he argues that these qualities are not to be found in "mere thinkers," those who get all their ideas from books, don't think for themselves, and are therefore unable to develop their nature to the fullest possible extent.
What Emerson is concerned with here is the tendency of so many people in society to go with the flow instead of doing their own thing and expressing their individuality.