Regular, real/official, taxi's are easily recognisable by their number plate which is orange with black letters whereas regular vehicles are white with black letters.
You don't have to use fake taxi's, that's your choice. A regular taxi ride in Stockholm and a Uber ride (depending on the time of day) usually don't have a big price difference between them. Unless you want to take one of the Tesla taxi's.
And taxis sometimes are cheaper than Uber here. I just moved apartments and paid 400 SEK for a taxi van to carry most of my boxes from one part of Stockholm to another, Uber XL was quoting a fare between 550 and 620 SEK.
I don't think that problem is unique to Stockholm, plenty of other cities have that issue.
Usually when I go to a new location, doing a Google search or two on these things proves helpful. The number plate stuff is on wikipedia and the VisitStockholm.com website for example: http://www.visitstockholm.com/en/Good-to-know/Getting-around... has all the information on taxi's, how to recognise them, what the regulations around them are and other methods of getting around.
A little bit of research upfront can spare you many unpleasant experiences no matter where you're going and regardless of if you know a local or not.
The issue is that there is no meter on the "fake" taxis. In other countries, you can easily tell if you're being ripped off based on the meter. If it's off, then you can be 100% certain.
You don't have to use fake taxi's, that's your choice. A regular taxi ride in Stockholm and a Uber ride (depending on the time of day) usually don't have a big price difference between them. Unless you want to take one of the Tesla taxi's.