If you're coasting down a rather steep hill in CVT mode, it will down shift for you to engine brake. That may be what you're hearing. This feature can be turned off by a dealership.
There are very, very few 6MT 3.5s out there. You might find a couple of them per year that hit the market. When I was buying my 3.5, there was not a single 3.5 6MT west of the Rockies. Others were unable to find one in the entire United States. If you were going to get a 6MT, you were probably going to get a 2.5. Your other option would have been to order one new from Nissan and wait 3-6 months to have it made and pay ~$30,000. The 6MT is actually more expensive than the CVT by a few thousand. So I don't think you made a bad decision at all.
You will also realize that although the CVT feels sluggish, it's actually faster than all but the best MT drivers. Lately, I've been experimenting with shifting techniques that involve starting in manual mode and ending in CVT mode to get 0-60 times that were previously unheard of on the Altima.
The main benefit of the 6MT is the ability to push a turbo to above 6PSI without concern of overheating the transmission. Other than that, you're golden. The manual mode lets you select gear ratios, and you can still have your right arm free to do... whatever you high school kids do with it.
