*SPOILERS INCLUDED*
I loved this movie as a child and love it even more as an adult. IMO it is not the alien scenes that bring down the movie a bit but the movie's unfinished ending. The alien bits would have made much more sense if the film had been completed and they had been better explained.
Each of the three boys in the film had his own storyline and his own lesson to be learned from his journey. They are each drawn into their adventure into space by the dreams they have been having and each has his own fears and expectations about the trip. But when they finally reach their destination and meet the aliens, they are in for a complete shock and find something entirely different than what they were prepared for.
Ethan Hawke's character lives almost entirely in daydreams and seldom acts on his dreams and desires. (In fact, he can't even work up the courage to ask out the girl he has a crush on.) River Phoenix's character is a science geek who is highly skeptical and somewhat fearful of new experiences and of life outside his family's lab. Jason Presson's character is a rebel with low self-esteem and difficulties with his dad.
When meeting the aliens, one learns to not take so much for granted, one has an unexpected adventure and flirtation with a troublesome girl alien, and one learns to believe more in himself and also learns a bit more empathy for his dad after meeting the father of their alien friends. If the film had been finished, the final act of the movie would probably have been about the boys applying the lessons of the story to their lives back on earth and to the supporting characters around them.