The Rubicon Express kits are probably one of the more "complete" kits offered on the market right now...that being said, your desire for ride quality will come into play here quite a bit. You obviously have a couple different options in this regard.
1.) would be to go with the IRO kit and enjoy the flex and ride quality that comes with a long arm set-up. However, Ive never been a fan of 3-link systems, just from a strength standpoint. 4 links will always be stronger than 3.
2.) like 4.3LXJ said.... stick with a short arm kit and go drop brackets. This isn't a bad set up really, in fact there are many XJ's running these in competition circuits (like team NAXJA at the King of the Hammers) ....granted, you'll have to be a bit more technical when it comes to tire placement when wheeling, but in my book, that will just make you a better driver.

Speaking from experience, doing a lift in phases is a great way to learn the jeep, the systems capabilities, and grow your own skill level in that particular vehicle. The one drawback to this is of course money spent over time, and upgrading certain components later while other are worn in the mean time.
You ARE on the right track though with choosing systems with full leaf packs. This will benefit you greatly in the long run. If price/budget is the one determining factor in what direction you'll be going, all I can say is really consider WHERE you want to end with your build. I had once said, I will never need anything more than 31's on a 3" lift....here I am today on 33's with 5" of lift.... thing change, and your build should take this onto consideration from the start.
Another avenue to pursue would be to focus on things like armor, recovery, gearing, and of course maintenance (ensuring the Jeep will continue to run STRONG for years to come) before you lift. A budget boost (spacers up front and shackles or SMALL blocks in the rear) will "get you by" as you add weight to the rig with things like sliders, skid plates, and bumpers/winch. Then your rig will be fully prepared for the kind of terrain that will open up to you with larger lift and tires.
Other things that you'll need to consider when planning a build is going to be the driveline...almost always, when lifting above 3" or so (and wheeling it), you will need to install a slip yoke eliminator kit (or SYE for short) and potentially shim the rear end to improve pinion angles...all this will not only strengthen the drive train, but will eliminate driveline vibrations as well.
I know this is a lot to take in, and honestly I could go on in depth much more than I already have, but if you take one thing away from all this more than anything, would be to do your research. You're off to a great start here, but get some face time with guys who have gone thru all this before, and get a chance to see some builds in person, and talk to the Jeepers in your area about their own experiences and advice.
Nothing beets a good afternoon of "talking Jeep" in person.
Good luck.