Aquarius is okay with two players, but it's not very exciting, because there are really only two elements being built.
I came up with these two-player variations:
Each player gets two Goal cards. The object of the game is to fulfill either of your goals.
The Trade Goal action is slightly changed as well. When you play this, choose one of your goals, and trade it for one randomly-selected goal of your opponent.
Each player gets two Goal cards. The object of the game is to fulfill both of your goals at once, with a total size of 10 or more.
For example, say your goals are Fire and Water. If the largest Fire group is 6 panels and the largest Water group is 4 panels, then you win. The two groups do not have to touch.
The Trade Goal action is slightly changed as well. When you play this, each player chooses one of his goals to trade.
Note that the two games have different Trade Goals actions. In Gemini, I've found, each player concentrates on one goal, so Trade Goals lets you unload your unbuilt goal while giving you a 50% chance of getting a well-built goal. But in Pisces, both players are working on both of their goals at the same time... so Trade Goals gives both of them a dilemma about which goal to give up. Which is much more fun.
Note that, unlike regular two-player Aquarius, two Trade Goals actions do not necessarily cancel each other out.