I wouldn't consider the Ultimate 12 for two... I have taken my youngest son with me before, it worked, but wasn't ideal, and I'm only around 5'7"... I wouldn't consider taking my wife in it. Just isn't big enough for 2 people unless you're both under 150 lbs and short. Even then it becomes a question of balance. (My opinion).
However, I do recommend the U12 big-time for solo. I did get in-seat time in the Commander but preferred the hull design of the Ultimate--better for standing, etc. For ME! Others like the hull of the Commander. It is personal preference all the way.
As well, I did not like the seat of the Commander. The Ultimate "First Class" seat is far more comfortable to me. The perch is nice on the commander, but I built a simple, under $10 seat riser for my U12 that is perfect and light. A breeze to paddle from elevated position, and simple to stand from.
Advantage of the Commander is that it is ready for a trolling motor due to the flat back. I had to make a mount for my Native, but love how it works. I use a motor pretty much to get me places faster, and also because I suffer from fisherman's elbow (both elbows) and paddling can be painful.
It is a personal preference. Wilderness Systems is a big dog in the industry, Native Watercraft is a small dog... not that it matters, but each has excellent hybrid systems and after-purchase support. Both have great communities where you can get tips and such.
Now if you want to go solo, and occasionally take someone, consider upping to the 14' model. Will give you a little more room for an extra body. Will add a few extra pounds, but still car-toppable.