Advantages of SOT Packages

For hand-soldering and prototyping, SOT (pin spacing 0.95mm) is easy to work with, easy to probe, easy to layout (you can route traces/vias under it).

SC-70 is smaller (0.65mm spacing) and this is the point where it does get annoying.

SOT-563 is even smaller (0.5mm spacing) and does not have gull wing leads. Hand soldering this one sucks. You can drag solder a large IC with 0.5mm pin spacing, but these tiny buggers are just a pain.

Thermally, for example SOT-563 does not have gull wing leads:

So it sits directly on the PCB. The path that heat has to travel to get from the chip to the pads and hopefully into the ground plane is a bit shorter than for SOT, so it has a bit lower thermal resistance than SOT (200 vs 250°C/W). Also the one in the picture above is thermally enhanced, the longer pin in the middle probably has the chip sitting on top of it, and it can be soldered on a thermal pad on your PCB. That's pretty rare. I'm sure you can find SOT-23-6 with the same feature, after all SO packages have thermal pads too.

For the same reason SOT89 can be quite good thermally if the back of the chip is directly on the copper pad on the back of the package, which is soldered to the PCB, but not all SOT89 packages do this.

SOT223 is larger, but the heat has to flow along the length of the leg, which is a handicap.

Anyway. For production, there are many other reasons: cost, ease of keeping things in stock... for example the PCB assembler has a bazillion MMBT3904 in SOT-23 in stock, because everyone has those. For less common packages, maybe not. Also think about yield. For example if the board is wave soldered, 0.5mm pin spacing is not really your friend. 0.95mm pin spacing has lower probability of solder bridges. If your board does not need to be very compact, not going for the smallest package allows more slack in mechanical tolerances, less risk of shorts, etc.

For prototyping or in an academic environment there's not really an advantage. SOT or similar is small, yet easy to hand-solder.

Other than that, for production different things could influence choice. Mostly cost. Economics are a funny thing and often you intuitively think one package is cheaper, while in reality it's the opposite. Hand solderability is a non-issue in this context, but things like thermal performance might be.