I made the change to a 4th gen from a 3rd gen.
I had a '99 SR5, 5 speed, manual, with e-locker. It was IJM and the Highlander edition. I owned it from 88k to 190k which was 10 years.
What I liked: It was a solid truck. Had decent room and power. The manual was really nice for loaded mountain driving and I had no issues with it on or offroad. The Highlander had no chrome so that combined with the classic body it was a good looking vehicle. In the 10 years I owned it I lifted it, built skid plates, installed sliders, lights, radios, etc. Maintenance wise I got really lucky. I kept up on most items but never did a timing belt/WP or clutch. I had many little things I did have to tend to though such as the starter contacts, axle seals and bearings, malfunctioning tailgate, leaky seal here and there, injector, A/F sensor, and a few other things. For the most part I did more work just keeping up on maintenance and keeping it clean.
What I didn't like: There wasn't much I didn't like. For the most part I was getting bored with it. It's not like I was looking for something else to mod on it (I felt I was done and just used it) but I was wanting something else. The ride was a little rough (5100 & OME) and at times it felt like a rickity old vehicle with little clatters and whatnot.
The 4th gen: When I got an idea to replace the 3rd gen I began wondering what I'd get. I don't care for the 5th gens but looked at a few. I also looked at GX470's. 4th gens have never been a must have vehicle to me, I don't know why but maybe it's because they were getting popular when I had my 3rd gen. I know many who have 4th gens and drove a few and ended up getting an '07, V8, 4wd, with the 3rd row. I've got two kids so the extra seating and interior room was appealing. So was the extra power of the V8. Those right there removed the boredness I had with the 3rd gen.
The 3rd row option in the 4th gen give you rear seats different from the regular seat configuration. In my case the "middle" row reclines. That along with the extra width and leg room makes it a ton more comfortable. The 3rd row is actually just two seats and they are low to the ground so they are not comfortable for adults. The kids like them but I don't use them much. The 3rd row option also has a different floor and the middle row of seats roll forward which results in a cargo area shorter than me which makes it hard to sleep in whereas with the 3rd gen I had enough room to lay down.
The 4th gen is heavier and "awd" so the feel is different. It's much smoother, quieter and fun to drive though (even being an auto). I've got sliders, skids, and a Dobinsons lift and I'm really happy with it. It's still very good offroad but does have lower hanging plastic bumpers that I worry about. I don't want to add large bumpers to the 4th gen so we'll see what happens.
Like mentioned above, I got off easy on not doing a lot of the expensive maintenance items on the 3rd gen. I've owned the 4th gen since January and recently had the WP go out so I had a forced t-belt and WP service done. I've also got a torn CV boot that I'll need to deal with. Both vehicles have the pros and cons (which will be different for everyone) and their common issues. T4R is a great resource though and will help you along the way.