It just seems like they could've tweaked it some more or made a new version of it to keep that smooth inline feel. And I'm sure Jeep isn't the only manufacturer to kill reliable engines for seemingly no good reason. Its like the big board members at these companies say, "What? It runs good? Its proving to be reliable? We certainly can't have any of that! Kill it!"
Inline six engines are just not a great choice for a variety of reasons.
1) Packaging. Fitting an inline six into a FWD vehicle is incredibly difficult. When Volvo shoved a 2.9 litre I6 into the S80, they had to develop the world's thinnest transaxle to make it fit within the width of a full-size executive sedan. IIRC the only other company crazy enough to try an I6 in a FWD car was Daewoo (sold in the US as the Suzuki Verona) and they've stuck to very small I6 engines that are handily out-performed by competing 4-cylinder offerings.
Even in RWD vehicles, an inline 6 is still generally the longest engine fitted, necessitating a longer hood or the sacrifice of some interior volume to accommodate the engine. A V6 or even a V8 will make much more efficient use of space within an engine bay, regardless of whether the vehicle is FWD or RWD.
2) Expense. Since packaging pretty much precludes installing an inline six in a passenger car (at least, for mass-market vehicles, luxury marques can absorb the engineering costs and pass those on to consumers and where the prestige makes up for any lost interior room), any manufacturing savings that might come from being able to run an I6 down the same production line as an I4 are essentially thrown out the window. For most companies, an I6 really only makes sense for a truck, and you don't want a truck engine to be based off the same modular design as the 4-cylinder in your company's subcompact.
This essentially means that if you want to have an I6 in your light truck line, you need to have an entire, separate production line dedicated to one engine. That's not good. With a V6, you have more options. Either you can run a 90-degree V6 down a shared production line with your V8 engines or you can have a separate assembly line for 60-degree V6 engines that are middleweights and can fit into your family sedans without packaging concerns as well as into your pickups and manage with being engineered for medium-duty applications.
Basically, I6 engines just don't make economic sense today except in very rare situations. In Volvo's case, expanding their existing I4 and I5 engines into an I6 range and solving the engineering issues was cheaper than building an entirely new line for a V6 engine family. (Volvo's V8 engines are built by Yamaha, so Volvo avoids the cost of a separate assembly line for their V8s.) Also, Volvo only puts the I6 in large cars to begin with. BMW, the only other major user of the I6 engine, sells based on being a "premium" car and they can easily pass the cost of the engine on to consumers; BMW also is widely known for having less interior space, but, again, given their market, that's not a real issue.
Other than situations like those above, it just makes far more economic sense to use a V6. It's cheaper and the engine can be used in far more vehicles in far more situations.
ZV