The latest two vids call for some comments, I guess.
I have never had a problem with mission 2. You have to scan the container, disable the freighter, then dogfight. Even when I ordered wingmen to protect the freighters, and joined in, it all came down to dogfighting, far away from the freighters (just like in your walkthrough). In many of my playthroughs, I simply ordered everyone to either defend me or engage the enemy, and fought until the mission ended.
The "invisible" fighters are Ptahs, who are stealth fighters armed with Banshee Xs. There will be some more Ptahs in the campaign as well, so if you get EMPed, look behind you and you'll likely get across one or two of those guys.
The dogfighting part was much longer (and bogus) in the original version. Apparently, even now when they jump out once the freighters are down/escaped. It wasn't rare, in previous versions of the mission, for the mission to drag on for 12-15 minutes, 7-10 of which was destroying Horuses.
The debriefing is indeed faulty. It was present in the original and left in in the rebuilt version, so it's partly my fault too. I don't recall changing anything in the briefing texts apart from spellchecking.
Mission-wise, I was primarily interested in fixing mission-breaking bugs. You'd have broken mission 2 in two of your playthroughs had you played the original.
As for the freighters:
I'm aware that it's strange that Freighter 1 happens to contain Icarus. In the original version, the freighters were given default names, and Icarus was in Ma'at 17 (no, not Bes 17). I advised Shadow to change the freighters' names, which he apparently did. I didn't complain, because I was concerned with getting the debriefs and the campaign file work right. I'd rather see people compain about a freighter's name than complain about getting a success debrief and not able to progress in the campaign.
Mission 3:
Looks like the release contains an older revision of the mission. The spelling errors (like "breifing") and that damn comma in "Get cracking pilot" were fixed in the latest revision, and there should be also a "Wait for Transport to Dock" directive.
About the Weapons subsystem: You have to tag it so the fleet knows where the Queb is, and you have to destroy it to disable its beams, like it is said in the briefing.
Generally speaking:
It's good that you're doing these video playthroughs, so thumbs up for your efforts, Lucika.

Now we can see it through the eyes of one of our players. I'm certain that these videos will be useful for CoW2.