Perhaps he may be clueless to his surroundings in the beginning, but how does that make him happier? It's noticeable that he is embarrassed at his low intelligence in the beginning. If he enjoyed the way he lived, why would he want to change?

Toward the end, he also had the satisfaction of the discovery of the Gordon-Algernon Effect.

Charlie was arguably happier in the end, than in the beginning. In the beginning of the book, Charlie was constantly harrassed and insulted because of his low intelligence. Even though Charlie began to lose all that he has gained towards the end, he will always have the satisfaction of uncovering the Gordon-Algernon Effect. The satisfaction and pride is sufficient to show that Charlie was happier a post-intellectual than a pre-intellectual.