one major issue with zotero is the lack of android support. they are working on an android version or app or something since forever.
then is the way you store the pfds. if you want to sync between multiple computers you have to either know how to work with webdav or know how to point zotero at the location where you have your pdfs or (what they most certainly love) pay a lot of money for not so much storage space on their system. that last thing is what i don't like because i just don't trust anyone these days. you get invested in a system, build your routine around it only for them to shut it down, sell it watever and then puff you have to start over.
people keep calling zotero foss but if they were truly foss they would have a much more transparent way for people to roll their own selfhosted zotero server. instead, what they have is a dump of an old version, with next to zero documentation and a bunch of stubborn people that have managed to get something working but not quite.
I get that they are trying to make money but I am sure they could do that and be more transparent.
The other thing is the reliance on so many plugins. While zotero itself may last a while, who can say anything about the many devs of the many plugins that you end up relying on in order to make zotero bow to your routine? I like zotfile and a few others, but how long are they going to last? Also, reinstalling my system is a huge pain to get back to my routine because I have to remember all the settings for each and every plugin I install. They should come up with a way to save all these settings and restore them, and no don't do it through another plugin!
the problem comes from scientometrics. you have to pump up your numbers as a researcher if you ever want to get that grant, or that promotion or that tenure position.
there was a time when there were far less journals and articles published per year. people spent a lot more time on an article and it shows. read an article today and you are left with nothing. back in the day (and by that I mean before about 2010) you had everything you needed to understand the subject and form your ideas. today is about tonnes of references (and not the useful kind either!) and inventing catchy acronyms.
but now that scientometrics is so important everyone is chasing the numbers and not the quality. you need that high impact factor up, that h-index, the influence score and the citations up. and since you have no chance to spend more time to increase the quality of your article, the next best thing is to increase the quantity you push into the grind. these predatory publications are precisely the answer to this artificially increased demand. yet people continue to be surprised.
think about it for a second: consider how many PhDs are awarded each year, they have to go somewhere and most of them want to go up. hence the increased demand. PhD courses are a huge business for universities, and this business drives the publishing industry. mix into this the fact that in academia, you have to change your research subject about every three years to keep it real for the grant masters with the big project money, you get to this disaster today.
try to build a bibliography today on a new subject and you will find tonnes of articles and then try to find the ones where you can actually understand where the science on that subject is at.
i don't know what the solution is, but counting scienctometric indices is not it.