1. if you don't abort, you will get all equipment form i think second misison.
2. they are not the ones using the MC. however they do have a lot of movement and will actually be used as scout. take any alien out as fast as you can and move or hide.
MC is used either by tasoth (reptile kind of guys) or aquatoids (little green ones). in XCOM they usually need to see you to use MC (note: sometimes you can see things through walls :blink: ). my advice is (if this is your first time) to save the game each turn under a different file name. that way you can seek out the aliens, reload appropriate turn and bomb them.
in ship second mission i think on beginning it's preety much safe to toss grenades among those boxes, because that's where they are usually hiding.
as for the aliens you mentioned - yes they are a nuisance, because they explode and have a lot of shots available which are quite accurate. my advice is to try and use some sonic grenade on them or other powerfull explosives. also HE clips in gass cannon make targeting a lot easier. sure they blow up half of the house on terror sites, but who cares. it's not like you will have to pay for the damage you do