Weirdly, I love examples that fall in both camps, ATC (cottage, but pro), and Dynaudio, whose new research facility looks set to give Harman a run for its money:
I agree in principle that larger sciency manufacturers should give the best bang for the buck, and that they have the most resources for developing good speakers. Still, I have found myself drawn to smaller manufacturers lately. It is as if the big guys stick with the conventional, and don't really break new ground.
Some examples: Harman owns the patent to CBT speakers. But they never commercialized them for the home market, in spite of their obvious theoretical advantages (there's a reason why they're common in PA). No large companies make line sources at all. No large companies do omnis or dipoles, in spite of the theoretical advantages both omnis and dipoles can have (read Linkwitz). Out of the large companies, only Klipsch makes large horns, even though horns
can have theoretical advantages as well (and the best horn speaker Klipsch ever made, The Jubilee, was quickly withdrawn from the home market). Two of the most innovative current DSP speakers - Kii Three and Dutch&Dutch 8C - have sprung out of independent manufacturers. And how about electrostats? Not really produced by the biggest players either. (as for me, my current AVI monitors sound subjectively better to me than most of the active monitors I've heard from bigger companies)
There are some exceptions, of course. B&O have made real innovations with the Beolab 90 and 50. The active Dynaudio XD series is good. Etc. But it doesn't seem to me that the larger companies, on the whole, have been pushing the envelope very much. My take-away is that the large companies is the place to go if one wants good quality within in the conventional speaker paradigm - forward firing box speakers, that is. But if one prefers non-conventional speakers - as I often find myself doing - one needs to look in other directions.