The best all-around Toyota truck brakes come from using all Toyota parts. Their pad compound's friction vs. temperature curve is the best match for truck use. Their rotors meet the thermal dissipation constraint that Mr. T intended the brakes to have.
There are very few "upgrade" parts out there that don't improve one aspect of performance by compromising some other aspect. If the Stop-Tech rotors mentioned in the article do still weigh more than OEM rotors then those would be a good option. As long as the increased unsprung weight isn't a concern, which is unlikely in a truck.
Brake parts from the local big box auto parts store will certainly cost less. There is a very good reason why. Those parts are not as good as the OEM parts. They won't last as long and work as well as the OEM parts.
There are threads and articles out there about putting Tundra brakes on Tacomas. I am unfamiliar with any of them. In general making this change results in a larger rotor diameter and one that is thicker as well, which will increase brake torque, thermal dissipation, and unsprung weight. However, to make it all work there may be some compromises that have to be made that are either individually unacceptable or are not good practice (like grinding on a caliper body!). Proceed down that path with caution.
