Once upon a time, I bought a brand-new '89 YJ (the "S" model - which was the super -stripped down entry level one) with the 4 cylinder and manual transmission.
That thing was full of problems - had bad pistons and wore out the syncros way too fast...but I LOVED that thing. It was super easy to work on (had one of the cleanest engine bays I have seen on any modern era vehicle - largely due to the throttle body replacing a carb and electronic ignition replacing the points, etc.)
I think the weak spots are:
Rust - check the body, esp the floor board area for this.
The front seat brackets broke/bent easy (of course I am a pretty heavy guy, so maybe it's just me
)
I think the assembly that controls the heater/defrost/etc is hard to come by if you had to replace it (check with the guys in the YJ section to be sure if you decide to get one.)
The clutch assembly was located/designed in a way that meant you had to do a lot of work to replace the clutch (I think this got redesigned in later YJ's, but would confirm with those guys if you go that route.)