Like you, I too was between the Nova and the SXP just two years ago.
Today, I own the SXP (with the 3.5" chamber and 28" barrel) and love it. Smooth handling, cycling gun. You really won't find a smoother pump action than the SXP, unless you get the Browning BPS, which is in a price category of its own in the pump action market.
If you are not likely to hunt much waterfowl, I would strongly suggest going with the 3" chamber instead of the 3.5". The simple reason is you can buy a rifled slug barrel with the former, but no such barrel exists for the 3.5 SXP chambered model. I don't use a shotgun for deer, so this doesn't negatively affect me---but with you planning on using it as a primary deer gun, the 3" seems to be a no-brainer. I chose the 3.5" simply to accommodate a heavier payload for turkey season. But with today's heavy loads and chokes, the benefit of a bigger chamber is frankly marginal until you hit 50 yards (and even then, you have to know how much to compensate for the drop). You'll be more than fine with a 3" chamber, then (and it'll probably save you a little money, too).
One thing I hated about the Nova, on the other hand, was how loud and gritty the action is. Even when not cycling it, I found it just rattled too much---same problem I have with Mossberg 500s, but much worse.
All that to say, I chose the SXP, and think you should, too.