Malmo, Kalmar, Uppsala with teenagers?

I haven't been to Malmö. If you have a car, then you can combine Kalmar with a stop in the glass region and some time on the island of Öland between the two cities. If you don't have a car, then I'd instead go directly to Stockholm and spend time around there. It has been 20 years since I visited Uppsala, but it is an easy day trip from Stockholm and if you want to see it, I'd visit as a day trip.
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As far as other destinations ... I really like Mariefred as a day trip from Stockholm. It is a small town on Lake Malaren where Gripsholm Castle is located. Gripsholm Castle is a pretty impressive renaissance castle and it could be a place that a teenager would find interesting if they happen to like castles. I also really like the island of Gotland, but you need to take the ferry or fly to get there. The town of Visby still has its medieval walls and there are some nice beaches. For water, you could also spend some time on one of the islands in the archipelago or take the overnight ferry to either Tallinn or Helsinki.

Thanks Virginia, any insight on Goteborg? We have to decide whether to travel on the West or East coast to Stockholm...

A caveat. I've never visited Göteborg or any of the towns on the west coast and my knowledge comes exclusively from friends and Swedish classes. My understanding is that the most scenic towns are north of Göteborg along the coast of Bohuslän. For example, Smögen is well-known. If you are a fan of Camilla Läckberg crime novels, then you will know of Fjällbacka.
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I have traveled along the east coast. If you are traveling on the east coast by car, I'd plan a stay either in Kalmar or Öland. I personally prefer Öland to Kalmar. If you are looking for a lunch stop between Kalmar and Stockholm, Västervik is a nice town on the water for a break from driving.
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Another option (if you have more time) would be to drive to Oskarshamn and take the ferry to Gotland and spend a couple of days there. From Gotland you can take the ferry to Nynäshamn which is a little less than an hour's drive from Stockholm.

I did enjoy Kalmar - compact, walkable, old town and I'm sure that teens would like the castle with Medieval furnishings. Also (while driving) enjoyed the Kosta Boda factory tour (which is also nearby to a moose park). On that driving trip, Soderkoping made a nice mid-way stop.