Hi, Eric. Been away from WikiTree for almost two weeks, so pardon the belated reply.
You're right: FTDNA is the 800-pound gorilla of yDNA and mtDNA testing, and that was one reason given for why they put no new money or effort into Ysearch or MitoSearch after around 2013 or so. Well over 90% of the data came from their own customers. They left the two sites alive, though unsupported, as a convenience to the genealogy community because there was a small fraction of results there that had come from out-of-business companies like Sorenson, or from Ancestry's first run at DNA testing when they offered Y-STRs through FTDNA's lab, and from companies that produce minimal output like Oxford Ancestors.
But the landscape is always changing and companies like YSEQ, as an example, are gaining some ground. (Genetic genealogy trivia time: FTDNA bought-out the assets in 2006 of a company called DNA-Fingerprint owned by Astrid and Thomas Krahn. The Krahn's moved to Houston and helped lead the design and building of FTDNA's Genomics Research Center. The Krahns subsequently moved back to Germany and in November 2013 opened YSEQ, which now offers yDNA testing panels, a la carte SNP testing, and even full-genome sequencing.)
I think there's still a need for the niche that Ysearch or MitoSearch served, and others do as well. Watch this year for developments coming from the direction of the folks who bring us DNAGedcom. Diane, Karin, Rob and company have registered the domain name "genetic.family" (it's live right now, but simply redirects you to DNAGedcom) under which they plan to expand their offerings. One of which is to be a combo database of both yDNA and mtDNA information. That domain name (which I won't specify yet because I don't know if it's been made public) was registered three months ago and Rob made mention of the new service in a presentation he gave a couple of months back. I believe the initial target was a September beta test, but I don't think they'll make that...at least not a public beta. But I have my fingers crossed that we'll see something before the end of the year!