They are quite different beasts, really. It all depends on what you want/like.
A good bit is cosmetic. On the CE there's no 10-top or mixed hardware; the birds are plain. For zero logical reason, the scarf joint bugs me if it isn't super well matched.
A lot is functional/tonal. CE should generally be the brighter guitar due to the bolt-on maple neck and steel bridge. The finish on the necks will feel different. The carved top on the CE is shallower; this is to save on production cost, but I actually find it a lot more comfortable and sleek than the deep carve of the Custom. The switching is different; I personally would take the CE controls any day, but others like the blade switch.
For me, if I liked skinny necks, I personally would pick the CE (and maaaybe upgrade to a Mann trem) because I don't care about the blingy stuff and I find the mapley sveltness appealing.
If the Custom is going to give you something you like better than the CE, then yeah it's an upgrade. Otherwise, meh, you're cool where you are. Different beasts.