you'll almost always get more out of it if it's stock. plus you can probably put a lot of the stuff on the new one. Do you like the mods you've made and parts you've installed? would you make the exact same purchases/mods on your next Jeep?
remember that you won't pay tax on whatever they give you for the trade. So if they give you (for example) $20,000 and the tax in your state is 10%, then your trade is actually worth $22,000 of the final price of the new Jeep. Which means you'd have to get more than $22,000 out of your Jeep in a private sale to be ahead of the game. Plus there's always the question of how much of a hassle you'll go through to sell it, and how long it'll take. Just some things to keep in mind...