From my experiences, TS seemed to be overkill for a lot of applications with which I have been involved, like "trying to swat a fly with a Buick" (to quote a friend). Add to that the additional cost of deployment/debug licenses for multiple test stations, the bill goes up quickly.
Learning curve also comes into play as TS has seemed to become its own programming language and is not as easy to learn as LabVIEW for those without the budget or time to take the training classes.
With a "roll your own", after the initial time investment of creating a test sequencer in LabVIEW, you can deploy to as many stations as you want without the cost of additional deployment licenses by just building EXEs.
Where I'm currently working, TestStand is just starting to gain a foothold, but ease of deployment and cost of deployment licensing has been a source of contention.
Now, my opinions are based solely on my experience with using TS on and off for several years without formal TS training. Ironically, a couple of my coworkers and myself are going to be taking a TestStand classes within the coming weeks, and I'm interested in whether my personal opinion (and those of my coworkers) will change.
At my previous employer, we still had a system running the precursor to TS: Test Executive. We had kept updating it until we ran into an incompatible version of LabVIEW, then just "froze it in time". Nobody there was very familiar with TestStand and how much it would take to do a migration as the station tested a large variety of boards. Because there was only one operating station, the risk of downtime for migration was considered too great, so it was never done. Test Executive seemed so much simpler and a better match for the needs at the time.
A second station was created to do the same as the one running Test Executive. Test Executive wasn't compatible with the newer version of Windows, and they still didn't want to go the TS route, so we ended up going with a LabVIEW-based test sequencer from CalBay (now Averna) called "iVVivi". I became very well versed in iVVivi and it was definitely simpler than TS. It also had an integrated LabVIEW OOP-based HAL, which was very attractive. However, in some respects it was TOO simple and required some creative LabVIEW routines to mimic some functionality available with Test Executive. I don't believe iVVivi is even supported anymore, so they may eventually be forced to go the route of TS. Or, beg NI for the password to access/update the protected VIs to recompile in later LV versions.
EDIT (3/2020): After having had the training and applying what I've learned over the past year, I can say that I understand TestStand much more, including its quirks. I still think that it could be suited for some applications, but still way too overly-complicated for the majority of applications that I deal with on the day-to-day and the additional costs per seat/deployment are still a deterrent. It still fits the "swatting a fly with a Buick" analogy I used before.