When designing a game's interface, you have to decide what are the most important/most frequent actions the player will be performing.  In GC2, those actions are, in order of importance...

-Panning Around the Map
-Selecting units, planets, other game objects
-Setting Destinations for your Ships
-Zooming In-Out
-Rotating the Map

The first three items on this list are necessary to playing the game. If these actions aren't available to everyone, in the easiest method possible, then the game won't be fun (or simply unplayable).

So, since the left mouse button is the primary one, we use that for the first two items (with a bit of logic to determine which action to perform). Setting destinations for the ships gets the right mouse button (universally known as the secondary button).

We're then left with the last two actions, which aren't necessary for gameplay (unlike in Homeworld) but still should be accessible to players at all times.  This is given to the middle mouse button, which a small percentage of players won't even have.  For this reason we've added keyboard commands or onscreen controls so everyone can still easily perform these actions.

Using the right mouse button for setting destinations isn't something we're doing as a throwback to GC1...it's that way because we believe it's the best choice for the game. In GC2, rotating the map is a fun diversion, but it really is just for fun, whereas setting destinations is a key element to playing the game, and should defiantly take precedence