Limited should have bed liner standard, delete is actually the option. I built my Laramie Longhorn to limited specs, 4 corner air, keyless, convenience package, sunroof, Nav, etc.
I absolutely love it and use most everything. Not the biggest fan of the Auto windshield wipers. And I do not use the Auto high beams.
As previously stated, the only real choices are bed size, 5' or 6.5'. Likely the short box as it's much more park friendly. I have the 6.5' and my wife cannot park between two cars. Then ram box or not, depends on your styling choice, and if you plan on a topper or the like, or hauling anything other than a standard ATV that you need more than between the wheel wells. Tonneau covers are available.
Tow mirrors, I like mine, many don't. But they are a hassle to park with because of the additional width and no power fold.
Limited slip rear is nice but a 3.55 is all that's necessary. Regardless of towing. Especially if it's Used for regular commuting.
Full cast aluminum rims if your in the salt belt will last longer but it's a $1500 upfit even on the limited I think. I don't mind the bezeled rims that come standard but they will pit faster