It's not that 4043 wire welds like crap....... in fact, 4043 welds are quite clean, while 5356 welds are sooty. This wire also produces a LOT of smoke. However, the soot and smoke is a result of the additional alloys added to 5356 to make it corrosion resistant.
Also, 4043 is a much softer wire (because it's pure aluminum, not alloyed) and as a result, it is more prone to jamming, especially in a conventional MIG welder. While you may be able to pull it off with 5356, you can forget about trying to run 4043 through 15 ft of a MIG gun lead, you'll spend more time digging bird nests out of drive rolls and cussing, than you will spend welding. For this wire, you absolutely have to have a spool gun.
When I first started welding, I worked for a while at an awning company. We welded a lot of aluminum frames. We used 4043 wire for all our work. A while later, when I started working on boats, another welder told me to never use 4000 series wire in a marine application. I unknowingly did it one time, to repair a corrosion hole in a customer's boat. A couple of years later, low and behold, same spot was leaking again, and the corrosion was worse. Lesson learned. Fixed it with 5356 and that was the end of that problem.
Preheat thick aluminum parts. Anything 1/4" or thicker needs to be preheated, or the bead will just lay on top of the material, and it will peel the first time you put a load on it.
And finally, always remember that aluminum is 1/3 the strength of steel. This means that when you are laying out your design, it will call for additional bracing, or at least additional weld points. Even so, there are some instances where welding isn't going to be strong enough. Take for instance most aluminum boat trailers. Note that cross members are usually U-bolted, not welded. This is because it's joining thick sections of aluminum together, and as mentioned, thick aluminum doesn't take a bead as well as steel. You'll find a lot of porosity as you're having to get the material so hot for the bead to lay flat. As a result, these welded joints can break. Bolting them eliminates the problem.