They are clear windows, and I think both are round or oval, not squarish.
Alien Conquest had blue ships and it worked. They didn't transform, they were well built, they mixed new LEGO style with old.
I think orange is my least favorite LEGO color, it's pretty useless. It's ugly if you add too much and it's rather ugly if you just use it and white. Plus white is boring. Aqua Riders was yellow, Atlantis was red (looked great with trans yellow), Alien Conquest was blue, Power Miners a little too much lime. Now we just get 90% white with black and orange. Ugh. I also hate orange on minifigures. At least one alien ship is lime green, dark red, black, tan, dark tan. Use some more colors to add life to the human sets.
It's just like Mars Mission, same color, the things transforms, and it looks rather blah.
It's hard to base a theme on one set, but the set does show the color theme and the basic design and I'm not impressed, more so after we could have gotten one more kick as series from AC.