There is in fact much to do to improve it FOR SPECIFIC MISSIONS. But if you don't know what that mission(s) is, you may very well make changes that improve it for some purpose you don't need, and in the process ruin it for other purposes. Somebody a few weeks ago had a thread on here for a few days called something like "Help me not ruin my new JK" or "How to mod without ruining?" or something like that. It was a good, honest original post talking about how that individual had been down this road with previous Jeeps and wanted to not do all the things most people just do "because it's what you do to a Wrangler."
Case in point: lifting 3.5" above what Jeep engineers designed the rig for will absolutely, positively, without question have a negative effect on the car's road performance. Handling will suffer, mileage will suffer, noise will be greater, acceleration will be reduced. Can things be done to mitigate these problems? Yeah. But the fact remains, if you did those things to an unlifted Jeep, it would still get better mileage, be quieter, accelerate faster, etc.
People will now come on over the next two pages and excoriate me over this statement. "I have a 3.5" Stone Stomper Dual Reservoir PentaShock Air Damper system with TreadTramper MT38s and it rides like a Cadillac, gets 35mpg, and I have to check the speedo to even tell if I'm moving it's so quiet."
And maybe they do. But I would suggest that if they had the same shocks and springs and tires, but at stock ride height and stock tire sizes, the Jeep would handle and ride all that much better. They may have managed to retain the Wrangler's (fairly crappy) OEM ride and handling with the 3.5" lift, but they could have improved it greatly with the same dollars thrown at a Jeep with stock ride height.
Now, before you dismiss all that, don't hear me saying not to lift -- my Jeep is lifted (a modest 2" though.) There are certainly reasons to do so. The reasons, honestly, might not extend beyond wanting to look cool, but that's as valid a reason for a lift as wanting to climb Poison Spider Mesa. I just want you to understand that every one of those decisions you make to alter your Jeep will most likely have a negative consequence attached to it also. It will probably diminish some quality of your Jeep (there are a few exceptions). It will definitely lighten your wallet. So unless you can say, "I want to install the Dirt Digger 6" HiLift because I will be doing such-and-such with this Jeep and I'm pretty well convinced the 4" Grass Grinder version won't accomplish this," you may well be throwing good money after bad and make a worse Jeep out of your beautiful new rig.
Best of luck with her!