I have been working with a lot of thin aluminum sheet metal of 0.025" thickness, using a jigsaw with great efficacy. The cutting speed is not too slow, and the cut edges are very clean. There are no heat-affected zones; the jig saw does not produce excess heat that would effect the material properties in the proximity of the cut. There are some minor inconveniences however. The main one is limited maneuverability. As you may realize, a jig saw cannot do sharp corners or turns, but rather one long continuous cut. Also, sometimes when cutting from a large sheet it is inconvenient and slow to maneuver around, since for every cut you have to clamp down the work piece and shift the work piece around so that you do not cut into the table or whatever it is the work piece is resting on.
One of the most important advantages to the jig saw is that the tool and consumables (blades) are very cheap! The one I bought, pictured below, was only $30, with the set of 3 blades being only around $5.
I have also considered a plasma cutter. This much more high-tech option ionizes compressed air via an electric arc and turns it into plasma. The high-speed plasma jet is then used as the cutter by melting through the metal work piece very fast. Pictured below is one $650 model from Harbor Freight, which seems to be the most economical option for the average DIY-er. The advantages the plasma cutter has to offer is fast cutting and maximum maneuverability.
There remains questions for my aluminum sheet application whether the plasma cutter will produce a heat-affected zone and if the cut will be clean. I will have to try it out and report back later.
All in all, the jig saw is the best option for cutting aluminum sheet metal by far, because it is fast, cleanly cuts, and is extremely economical. I only considered the plasma cutter because I have a lot to cut, and I need it for other purposes and materials.