Lessee, a couple of things:
1. The initial mission, the "give space tech" one, only just got redone... Chris was trying to find a way to fix/replace the original version of the mission, with all the spy probes. I think it still needs work though, as it has many of the same problems. I personally think it's still going to need another overhaul... that mission type in general has been a problem since it was put in, actually. But yeah, it JUST got put in there in this new state, so it's a little wonky. Save and reload if need be, move slowly, get an idea as to how large the circle of shots is around the probes in general, and look for a moment when you can squeeze past them. Yes, it's irritating as heck, but you only gotta do it a couple of times. Do it like, twice maybe, and then stop. There's no reason to give tech more than a couple of times; let the others beyond that reach spacefaring on their own.
Feedback on this mission type would help as well (as in, on Mantis, or in the recent patch topic might help alot as well). Because it really does need work still, and it's the very first mission a player has to do.... so yeah, that'd be really helpful.
2. Even in tutorial land, you do have more than one weapon. You start with three, in any mode. When it's your turn, you give a movement command, and then it's time to choose a target. When you are choosing a target, the ability icons (which I think arent there in the tutorial...) at the bottom become replaced with 3 different ones; these are your weapon choices, and this is when you select what to fire with. Just to check, I went and had a look to make sure those are in fact there during the tutorial phase of Betrayal mode, and they are.
However, I'll make things really simple for ya: There's only two weapons you REALLY need to concern yourself with, this being the minigun, and the energy blaster. All of the others? You dont need them. You want those two. Right now, the weapons in the game.... ahhh, they're very unbalanced. It's not that those two are OP.... it's moreso that the others are all just basically useless against the current balance of enemies and such. It's not that they wont kill them, it's that they'll take 50 billionty years doing so. I very strongly suggest starting with the Acutian ship if this is your first go at the game (or if you're impatient like me), as it has both of those weapons from the start.
3. Tech development exists during the tutorial in this mode... it's in the friendly actions menu on your own planet. "Personal Dispatch: Technology research".
Beyond that, I cant help ya much. Most of my time has been spent working on the Obscura and the other new ships, which then also means LOTS of testing, which means not much time with THIS mode. Though some of the complaints you have with this one, I've indeed heard before from others. The bit with the tutorial and stuff mentioning the federation (I notice the voiceovers do this too...) definitely needs fixing. It might be good to open up a mantis ticket on those, as I get the feeling those bits there have been overlooked, what with all the other aspects to the expansion being worked on.
Though, what Eternaly_Lost says, I also rather agree with... it really does feel like this new mode is meant to be played only after the player has spent a good pile of time with Standard mode. Wether that's a good or bad thing, or intended or not, I cannot really say. Though, as it IS an expansion pack, theoretically people buying it would ideally be those that have already played somewhat... maybe.