I haven't used either of these phones, so I couldn't comment on the specifics.
I'm not sure if this link will work, but you can do a side-by-side comparison on PhoneScoop:
http://www.phonescoop.com/phones/compare.php?id[]=2763&id[]=2708&id[]=&id[]=&id[]=
The X is reported to have longer battery life.
X is LCD while the Incredible is AMOLED.
They both have internal storage (8Gb I believe) and a microSD slot.
Other than that, just like you said, screen size is a big one and Sense vs. MotoBlur.
The X is rumored to come with MotoBlur and the Incredible has SenseUI.
MotoBlur in the past has sucked, but this supposedly has a newer version, so only time will tell.
The other thing is Motorola vs. HTC. Some people prefer one manufacturer over the other.
App-wise, you should be able to install the same apps from the Market on either phone.