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It seems Toyota is having some trouble with their latest Tacoma, with engine and transmission problems being the most glaring. It's very 'un-Toyota', and hopefully isn't an indicator of slipping quality. My sister has a 2001 extended cab Pre-Runner which just cleared 105,000 miles without a single trip to the dealer for anything other than oil changes and her 90K timing belt swap. After hearing some bad word-of-mouth and reading about some bad press the Tacoma has garnered lately, she's decided to keep her bulletproof 2001 instead of buying herself some unwanted problems in a 2006. Neither of us are terribly fond of the Chevy Colorado style fender flares, so she's keeping Old Faitful, and I really cant' fault her for her decision.
Here's some reading for you:
http://www.consumeraffairs.com/automotive/toyota_tacoma.html
No offense, but the vast majority of the reviews in the article you linked to relate to previous Tacoma models, which have entirely different engines and transmissions than the current model. In fact, most of them are from the same generation as your sister's truck. I wouldn't judge any vehicle based on the quality (or lack thereof) of those particular reviews.
I am biased because I own a 4Runner with the 1GR-FE engine and five speed transmission, and it has been absolutely flawless. The 4.0L V6 is a workhorse engine specifically designed for light trucks, and it is being used around the globe in 4Runners, Prados, LC120s, Tundras, FJ Cruisers, Hilux trucks, and Tacomas. A destroked 3.5L version is being used in Camrys, RAV4s, Avalons, Lexus IS350s and ES350s, soon-to-be redesigned Siennas, etc.
I do not believe Toyota would put so much emphasis on an engine family if it were very troublesome. It is a modern design with impressive engineering and quality components. In addition, I frequent many 4Runner/Tacoma boards, and the only somewhat "consistent" complaint I have seen regarding the 1GR-FE is that it is a bit noisier than what some people expect from a Toyota engine. I have seen no indication of any significant engine failures of any kind, except one bad story on Yotatech.
The 5 speed transmission used in the 4Runner is the same transmission used in the Land Cruiser and Lexus GX 470 and LX 470. I am not sure whether it is the same transmission used in the Tacoma, but if it is, it would be one of the most proven, bulletproof transmissions available anywhere.
I say drive a Tacoma, and if it is what you like, buy it with confidence knowing that it will be at least as reliable, if not moreso, than any other truck in its class.