Agree with Vallejo Model Color, the design of the little capped containers goes a long way toward cleanly dispensing, and storing the paint over time.
You hit on one of the problems with conventional jars, when you pour over the side, paint inevitably gets in the threads and ruins the fit of the cap. That allows air to enter the jar and the paint begins to solidify to the gel state.
It's also not for the best to shake the conventional jar to blend the paint, that is not an efficient way for blending anyway. Plus, that brings so much material up to the caps seal and gets into the threads and rim of the jar, further preventing an efficient seal for storage.
I recommend stirring the paint only, that's really the only way for a complete blending, then once painting is finished the cap will be perfectly clean and will store the paint for a very long time. But Vallejo Model Air will solve your problem best, I think.
Patrick