Knock, knock... anyone heard of that Toyota recall???
Honestly it doesn't matter what brand you buy, they all have their own set of problems new and even more depending on how they were maintained over their life. Regardless of if you buy a Toyota or Jeep, it is all about finding the right one. Well taken care of, low mileage, maintained, etc. So many get caught up in the engine mileage (i.e. replaced engine so it's low mileage) that they forget everything else has xxx,xxx miles on them. Parts wear out and need replacing, no matter the brand. Some are cheaper to fix than others.
As for a Cherokee, they are great vehicles with a ton of aftermarket support and cheaper to mod than a lot of the other brands out there. As for best years to look for, if you really do your research you will find it most universally is '97-'99 models. This gives you most all the benefits of improvements, what is felt to be a better looking and function interior, steel hatch that is less prone to rattles or damage and a ton of other little things. If you don't mind the older style interior, the '92-'96 are the better ones. Without a doubt, a 4.0L is the way to go. Not a powerhouse in HP but lots of low end torque at low RPM's where you need it.
Cherokee's in stock for are very capable vehicles and really don't need to be modified to the hilt. Even a simple 3" lift, 31" tires will get you 90% of most places unless you really want to rock crawl. 4 door models are more practical with easier access to behind the seats and the shorter front doors make the hinges last much longer.
As for problems, overheating is one that comes up a lot but typically that is due to lack of maintenance. Jeep did not put a lot of overhead in the cooling system due to the short but wide radiator. This was a packaging issue of the body design. When everything is working correctly, this system works just fine but it doesn't take much to cause them to have issues. Typically plugged radiator, crap in the block due to using non distilled water, t-stats and radiator caps not being replaced when the system is serviced or just worn out, high mileage parts (like water pump).
I have owned a couple different Toyota's in my life and honestly had issues with both of them. The one that really turned me off of Toyota was our '90 truck with 22RE. At 90,000 miles the starter died. Shortly after that a front crank seal was leaking big time. Then at 110,000 it was burning a quart of oil within 3,000 miles. This was due to leaking valve stem seals and worn guides. It needed a head job and I sold it before I did that, telling the new owner what it would need. I won't even go into a very good friend, the issues they had with their Camry from day one.
Like I said, they all have issues. This being my first Jeep (after growing up with my dad always saying they should be called Heep), I have been very, very happy with our Cherokee. Minimal worked has been needed, my mods have been relatively cheap (compared to other vehicles I have owned) and it has gotten us everywhere we have wanted to go. I will also say it took me 3 months of looking every day to find the right one.
Good luck on your hunt.