These engines (both the 2.5 and the 4.0) are pretty much bulletproof if properly maintained. They don't have any real well known weak points except for the rear main seal on the 4.0.
The biggest issue that plagues all TJs is rust, particularly on the frame.
Highways. Highways will be the known problem lol! I have the 2.4l. Keep it light, don't go over 33 tires (I have 33x10.5) and I feel like I'm maxing out. Aluminum wheels if you can help it. Soft top all that jazz. Check out this thread on getting tips with our engines: Four angry squirrels, or the TJ 2.5's and 2.4's
Had the 2.5 5 speed in an old xj. It was rock solid with over 200k on it. Drove it for hunting and one annual trip was 300 round trip. Never gave a problem.
Hills in heavy traffic on the freeway. You'll do fine if you're zen about it. If you are coming out of a four banger foreign car, you're going to hate life until you get used to it. I think the original CJ2A had 36 HP or something like that. It makes me feel better about my SE when I remember that.
Like said above its a good jeep to start the addiction. Powerful enough to get the job done and have fun doing it. All you gotta do is be mindful with the mods, the lighter the better. All in all its an enjoyable little jeep