These two find each other fascinating to begin with. Aquarius is an air sign and therefore is a mental sign. Air stands for communication and of thinking processes, of learning, of exploration and of independence. These are all qualities very much a part of the Aquarian, character and experience. Above all, Aquarius is highly independent and very strong in its independence. It will not be pinned down. It will not be dictated to.
Capricorn on the other hand is an earth sign. What it looks for is stability and security and something that it can depend on. Its tendency is to take on authority. It is the sign in astrology that signifies success and being the one who holds the power strings. Capricorn is highly motivated, very ambitious, very talented, and is a controller. It is a domineering presence.
So, within those characteristics, you see that immediately once they get past the sexual stage they're going to be in this conflict over control. Who is in charge? Who has the authority? Who is in power? Particularly, Capricorn will try to domineer over Aquarius, who won't be domineered over. So, essentially they're going to run into great conflict temperamentally.
Probably, this relationship works out best as a friendship because then they don't get into that emotional interference with each other. They work very well as friends. They're both intelligent. But as lovers, they will run into that sort of passionate conflict that they will exhibit toward each other.