I'll write out something somewhat detailed, because it may help others too. We can't possibly tell you what the best setup for you is.
In general: the Cherokee is a very nicely equipped SUV that is more capable off-road than its direct competition.
First, comparing features:
Sport: You didn't mention this one, but it is the entry, no frills option. No V6.
Latitude: Feature-light version of the Limited.
Advantage: Price, 17" wheels accomodate a wide variety of tires.
Disadvantage: Some options not available... options which are very nice, and often outside of this market segment (affordable SUV/crossover). You have to add options to get basic segment features, like a backup camera. Does not have skid plates or a rear-locking differential, and therefore is not a true off-road vehicle.
Competitors (imo): Rogue, CX-5, Rav4, CR-V, Entry Forester
Limited (I'll try not to be too biased): Full-featured small/mid SUV. Advantage: Nicely equipped, lots of very nice options. The technology group is amazing, imo, and offers features which are typically "luxury". The luxury group is also notably "luxury car" feeling. Disadvantage
rice, 18" wheels do not accomodate a variety of good tires (I will buy 17" rims next winter for good winter tires) Does not have skid plates or a rear-locking differential, and therefore is not a true off-road vehicle.
Competitors: Loaded Escape, Loaded Forester, RDX.
Trailhawk: The only option if you really want to use the vehicle off-road, as it has the AD-lockand is Trail Rated. It is equipped for that at the base level, and can further be equipped to be almost as feature packed as the limited (for a few thousand more).
Advantage: Plenty of upgrade options, some pretty necessary, Trail Rated, looks arguably the best.
Disadvantage: Price, fuel economy, and cannot have some features, like HID headlights.
Competitors: None? It is pretty alone in mission - it's a blend of real off road capability and road manners, I'm not sure what else really tries to do that.
Next, the drive systems: I am not an expert on these things, so please correct me if I am wrong about my statements.
All Cherokees come with the 9 speed automatic transmission, but the gear ratios change somewhat based on engine and 4x4 system.
I4 vs. V6: Obvious difference, but somewhat dubious in value. The V6 has by turns been reported as "much more powerful" to "underwhelming" in performance compared to the I4, while the I4 has been describe as "plenty powerful," "very weak," and most often: "adequate." The V6 costs you 2mpg or so.
ADI: Either the Latitude or the Limited can have this option. This is basically a comparable four wheel drive system to most of the competition, though it is thought to be generally superior to everything but Subaru, and comparable to Subaru. Has different modes which can be pre-selected to give better performance in various conditions: Sport, Snow, Mud.
ADII:Again, either the latitude or the limited. "Off road suspension" like the trailhawk, and a more advanced mechanism for transferring power during 4x4 utilization. This 4x4 system is thought to be the best in the segment, hands down, excepting AD-lock. Has different modes which can be pre-selected to give better performance in various conditions: Sport, Snow, Mud. Adds active hill descent and 4x4 low modes for additional capability.
AD-lock: Trailhawk only. Incorporates a real mechanical rear differential locker and is generally considered to be a true (if entry-level) off-road-able drive train. Miles beyond anything competing in the same market. The trailhawk is aimed at a good blend off real off-road capability and on-road performance and comfort. Adds the pre-selectable mode: Rock, and selec-speed terrain for additional capability ("off road cruise control").
I bet I have made mistakes here, please correct me.