The Bulk Matter Transmitter seems rather disappointing. All that work, and all you get is two more minerals per city?
The Weather Paradigm, on the other hand... available early and makes a huge difference when you don't have a lot of Formers to spare. Awesome.

What are your thoughts?

As I exclusively play as the Gaians (and possess little need for non-alien military technologies), it would be rather difficult to provide just one that resides within the 'underwhelming' category.

However, with regard to satisfying secret projects, The Hunter-Seeker Algorithm comes to mind.

With each playthrough, a concerted effort is made to acquire it, as once obtained, I breathe a sigh of relief, and no longer have the need to worry about my bases being disrupted by enemy probe teams. I do not play the Alien Crossfire expansion; so, the negating effect of the Algorithmic Enhancement special ability is of no concern.

I can not overstate the positive sensation that is experienced when the following message is displayed:
"The Hunter-Seeker Algorithm has destroyed a [faction name] probe team!"

The best projects are far and away The Weather Paradigm, Hunter Seeker Algorithm, Cloudbase Academy, and Cloning Cats. You can also add Human Genome Project to that depending on difficulty - one of the best projects on Transcend, pretty bad on lower difficulties.

Unfortunately really just about every project from the final third of the tech tree is pretty unrewarding. Bulk Matter Transmitter is a lot better than it seems (it's actually +50% minerals at every base, the video and documentation are incorrect) but it's still pretty underwhelming, but still better than the Singularity Inductor. Clinical Immortality is basically worthless, and the Nethack Terminus is just sad.

There's also projects like the Living Refinery, Manifold Harmonics, and Self-Aware Colony that would be good in the mid-game but are almost entirely redundant by the time you get them.