Even though he isn't Basque, it just wouldn't seem right to see Samu in anything other than bright orange. He's been in with Fundación Euskadi since time immemorial.
Euskaltel definitely have the riders to put together a strong team for the Tour - but it would come at the expense of their team for the other GTs. They would rather contend for the Tour and the Vuelta than send Samu to France backed with Antón, Martínez and Nieve, and then possibly fail to podium the Tour, and then have no bullets in the gun for the Vuelta (though of course that may change soon with Astarloza likely returning).
Besides, Amets Txurruka crashing out in week 1 has meant we've seen far less of the orange jerseys than we usually do, if only because it's meant that 1,428 breakaways have been a man down.