I'm not yet sure there is a problem with massive clouds of t1 engineers, but assuming there is, I think increasing the build-rate of t2 and t3 engineers is the solution. Making them more mass/build-rate efficient would make them valuable later in the game for assisting. As it is, they are mainly used for starting a project and having a swarm of t1 engineers actually do the building work. The reason why you have 50 t1 engineers on a t3 factory (with all the problems that brings) is because they are the most mass efficient way to increase the build rate of a factory (approximately 3x cheaper than t3 engineers).
If my goal were to increase my build rate, making higher tech engineers more efficient would help solve the problem of unwieldy flocks of t1 engineers. As it is now, I only build the number of t3 engineers as locations where I need t3 projects built. There are many late games where I find myself spamming experimentals and haven't even built a t3 engineer because my commander is t3.
I think there is a natural value to having a unit with more higher tech schematics in its portfolio, but when only three t1 engineers has the same build-rate for 1/3 the cost, the ONLY value of the t3 engineer then becomes its schematics suite. The question for the community becomes whether or not we want t1 engineers to be the only efficient unit of build-rate assistance? Broadly speaking, my answer is no.
For this reason, I don't think changing the factories build rate is the solution because I personally like the strategic element engineer assisting factories add. If t2 and t3 engineers were building at the same mass/build-rate ratio as t1, then we could eliminate many of the current annoyances of 100+ t1 engineer factories because it would make sense to put fewer, higher build-rate engineers on the job.