I'll take this one.
Chemically, MDA lacks the additional methyl (carbon) on the amine (nitrogen) which MDMA has. As you pointed out, the difference between MDA and MDMA is analogous to the difference between amphetamine and methamphetamine; i.e., both MDMA and methamphetamine have the methyl group on their nitrogen, as opposed to the hydrogen that is the case with MDA and amphetamine.
Have a look at this image for clarification:
http://upload.wikimedia.org/wikipedia/en/7/77/Comparisons_md_analogues.png
On the left are (going down), amphetamine, methamphetamine, and methcathinone; on the right are their MDxx counterparts.
Pharmacologically, the difference is quite substantial. Methamphetamine's additional substitution makes it MUCH more active on the serotonin system than amphetamine, which is responsible for many of the differing psychological and physiological effects between those two. This also contributes to the greater potency and toxicity of methamphetamine.
MDA has more binding activity on the 5-ht2a receptor (the target of psychedelic drugs like LSD), explaining why it's generally considered to be more psychedelic than MDMA's relatively pure entactogenic effects (note that some MDMA is metabolized to MDA, which is why there are usually some visual effects with MDMA, though this could also be a result of the receptor being flooded with serotonin released by MDMA). MDA also releases more dopamine, meaning that many people find it more stimulating than MDMA. MDA appears to be more neurotoxic than MDMA; the full discussion on neurotoxicity of these compounds is beyond the scope of my time right now.
Wikipedia has a nice chart comparing the amount of dopamine, noradrenaline, and serotonin released with a slew of different releasing agents. Note that smaller numbers mean more neurotransmitters being released:
http://en.wikipedia.org/wiki/Releasing_agent
As to which one you prefer, it comes down to personal choice. Both can be wonderful or terrible, depending entirely user. As I already said, MDA is GENERALLY considered to be more psychedelic and stimulating, while MDMA is more entactogenic. Which you prefer really comes down to personal choice.
Hope this helps