1) I'm pretty sure that's correct.
2) They are cheaper and inferior overall, but still capable of taking a Mindy down. It's worth noting that Yamatai power armor is designed more around being light weight and agile, with it's main defenses being arm-mounted energy shields, so it's more of a 'depends on the abilities of the pilot' thing. The teleporter is nice, but it takes time to recharge.
3) They can both penetrate Mindy armor with enough effort. The Squids have shielding and extremely strong telepathy. The Nightmare is genetically engineered, well armored, capable of regenerating really rapidly, and can fire scalar blasts that can really ruin your day.
4) Yup.
Also, nice first post, by the way. ;I