Well, lets take this from the beginning. The AMC 2.5L is a Over Head Valve (OHV) engine. This means the valves are over the cylinders but the camshaft is inside the block. The crank is conected to the cam and the cam. Lifters sit on the cam and move the push rods which in turn move the rocker arms that push on the valves up top. In this system there are a lot of moving parts. This is why some call them tractor engines. With all those moving parts come vibrations and friction.
These engines typically make their power at lower RPM's but top out quickly. This makes them good engines for trucks since they need the torque to carry heavy loads and what not.
The 2.5L went though some changes since it's introduction in 1984. (Yes, it's that old.) First it was carburated and making under 100hp. Then in 1987, it went to electronic TBI. This gave the engine a boost and hp jumped to around 112-4hp. Then in 1991, the engine was given MPFI. MPFI raised to hp to 123. Torque was only 140lbs-ft and came up fast at only 3200 rpm. The engine is slectronically limited to 5600rpms.
For the TJ, engineers sacraficed a few hp for a smoother torque band. This is why the engine was down by 3hp compared to the earlier MPFI engines.
Now the 2.4L is a different beast. It's a new engine designed to be used on multi-platforms. Unlike the 2.5L, the 2.4L has an Over Head Cam (OHC). This means the crank is still connected to the cam but the rockers ride directly on the cam. There are no lifters or pushrods to deal with. This means there is less friction between parts, less vibrations and higher RPM's can be achieved. The down side is that OHC engines make their power the faster they run. So low end performance is a bit lacking. Overall, the 2.4L is rated at 147hp. which is a big jump over the 2.5L.
The biggest consideration though is with the aftermarket. The 2.5L has a limited aftermarket following. It was only for a few years with the Craftsman truck series. (No relation to the new series.) The craftsman trucks were all MJ's with a few XJ's. They were race trucks but were required to use the stock engine. This is where all of the performance parts development came from. The series was short lived and the parts were expensive.
Now since the 2.4L is used on several other vehicles. Most noteably, the Neon, parts will be plentiful. The 2.4L has already recieved a turbo from the factory which would make an interesting combo in a Jeep. Also, parts, like cams, pistons and other internal parts would be interchangeable. The Neon is a popular car and raced in SCCA.
If I had the choice, I'd choose a 2.4L but swapping in a 2.4L wouldn't really be worth it. The turbo engines fetch higher prices because of the Neon owners. Then you'd have to convert everything over to ODBII compliant. For all the work you could have installed a 3.4L-3.8L for less.
Although, for the best of both worlds, a supercharger or turbo would be a good choice on a 2.5L. You'll keep your own end power but boost the higher-end significantly. You'll probably make a lot more torque then a 2.4L Turbo.
