My new orange Renegade Latitude has a 1.4 6-speed manual trans. I admit it is slightly under-powered. My wife now wants one but in yellow, with an automatic trans. I understand the 9-speed automatic is a beast and causing quite a few problems with software and sometimes total transmission replacements. I am trying to talk her in to the manual transmission but she is being stubborn although she knows how to drive a stick. Any opinions out there? Automatic issues etc ?? Thanks 
Well my trailhawk is in the shop at the moment. Like a lot of the folks with drivetrain issues, so far all signs point to software issues and a possible power transfer unit failure to go with it. That's what the vehicle believes the problem is, and it disabled AWD.
What I can tell you is that with AWD disabled, the transmission is even smoother feeling than before, and still behaved like a perfectly healthy transmission based on my past experiences with other ATs that have experienced failure (i.e. diferent design, not the 9 speed).
So the downside is I'm a data point for powertrain failure. Upside is that it didn't leave me stranded on the side of the road.
At this point and time, I'm of the opinion that the only issue mentioned on here to date that is intrinsically an artifact of the 9-speed's engineering and implementation is the long 4-5 and 5-4 shift, which is due to it being the longest distance components in the system have to move to complete the shift.
I'm inclined to believe that most of the issues on the renegade are jeep software or the AWD system design. The vehicle had a few quirks I attributed to the 9-speed. One was a booming growling on acceleration. HAving had a chance to ride shotgun and listen now, I think that is just due to the fact that as an inline 4, it will have a point where it's exhaust generate an additive beat tone, and that unfortunately happens at about 1800-200rpm. Second was a whine on deceleration. With the AWD disabled, this doesn't seem to be happening anymore, which would imply it originated with the clutch pack back (this notion is reinforced by the fact that prior to having the ECU flip out and flag anything, that whine had gotten louder and started sounding like the straight cut gears you hear when backing up a car). Third was a propensity to engine brake rather aggressively. Granted once it cut out the 4wd, I didn't drive any farther than needed to get home and then to the dealer, but in those trips, no aggressive engine braking feeling.
There are way more instances of PTU replacement and control module failure/replacement as the end result of driveline complaints here than of actual bad transmissions that need replacing. If your worry is not having to interact with the dealer, I'd avoid it. The system as a whole is having teething pains, and at the very least is likely to go through several iterations of firmware updates IMO. If your concern is about being stuck in the middle of nowhere, I suspect the 9 speed doesn't differ much the industry norm. THE AWD setup might, but it has a failure mode that will allow you to hobble home.
