The area around the bridge on the river is protected because of nature (especially birds), which also creates problems to the nearby airport. Beside that, the other obvious problem is the cost: money has to be found in the general federal road budget, and a lot of other projects are fighting for that money. And as Ticino already received a lot of federal money for its infrastructures recently (the two new Gotthard tunnels, road* and rail, new tram line in Lugano, and other things), I'm pretty sure there will be a hard fight from other cantons to get their share. At the moment the project is thus stalled.
A road in the open air is a no-go because this 9 km x 3 km plain is basically the only flat area of significant surface of the canton, that most want to keep for agriculture, as a nature reserve and other needs that cannot be put in a tunnel like a road or railway.
I quickly searched for some statistics and they say 80% of the total terrain in Ticino is made of mountains, 15% of hills, 5% of flat land. Half of the area is covered by forests.
*I feel that Ticino would have benefitted more from the A13 missing link than from the second Gotthard tube, residents who go north of the Alps often use the train or travel by road on off-peak days, and in the worst case the Gotthard pass is a good alternative (except during Easter), while on the road to Locarno there is always congestion
für Güter die Bahn
pour vos marchandises le rail
chi dice merci dice ferrovia