Many deciding factors, and ultimately you'll need to pull the trigger yourself. Here's my thoughts, given I've owned both a 4th & 3rd gen
4th: Bigger/bulkier/roomier, smoother ride (possibly due to being newer), V8 option, more interior plastic, nice sport fabric seats, more electronics, projectors ('06+), higher vehicle purchase cost.
3rd: Smaller/compact, feels more like a truck, less electronics/gizmos, very simple, option of RR diff lock and/or manual trans (if you care for either), cheaper vehicle purchase cost.
I had purchased a 4th gen sport (V8/4wd) and loved it, but it wasn't what I was originally wanting (3rd gen). Eventually purchased a 3rd gen and recently sold the 4th and couldn't be happier. I prefer the older look and feel of the 3rd gen, possibly due to coming from a 1st gen Tacoma (which is somewhat comparable in generations).
Given you've now driven a 4th gen (I'd drive the V6 & V8 to compare), go and find a solid 3rd gen to test drive. You'll gain a good understanding of the above facts and it'll help your decision making process.
Also, as for the 4th gen that you've test driven, what exactly do you mean by the climate control being messed up? Was it simply just the lighting being partially out, or was the actual digital display (numbers/text) not working. If it was the lighting, that's a simple fix of replacing the climate control bulbs, which is common on both gens.