I've never actually had a 42RLE, but this argument is one I've also thought about for a long time.
I really don't see why having that 4th gear is really such a disadvantage. It only adds capability, and doesn't take anything away. In general, the more ratios and the wider a spread a transmission has, the more utility it has. Sure it may result in different axle ratios to be able to use all four gears effectively, but you still have additional utility over a 3 speed. Okay, if you're not regeared, maybe you have to press a button now and then. But it's an extra option (hence extra utility) you have.
Automotive manufacturers in general are pushing towards more speeds and wider ratio spans in transmissions. Not only does it improve fuel economy, but it also significantly improves the capability and the performance of the vehicle. The vehicles can pull slower, accelerate faster, pull harder, and run higher top speeds. Combine that with the fact that engines are becoming excessively powered, and you can get some crazy good performance out of modern cars even on the less expensive side.
I would bet a lot of money if you could mate a TJ 4.0 to a Ford 10R80 or GM 10L80, it would absolutely dominate any existing transmission (automatic or manual) on the 4.0 in driveability, acceleration, fuel economy, and pulling power. And realistically you could probably run any axle ratio from 3.73 to 5.89 on 35s and still probably get better performance than any existing 4.0 transmission with any axle ratio of your choice.