I honestly haven't found the missions... excessively difficult. They are really meant to be challenges. If you go into them underprepared, that's... well, that's your funeral.
The only stupidly difficult one for me was the robot. Its spread attack is very hard to avoid, and I hadn't thought of using a two-handed sword for that purpose. Other than the damned spread attack, the rest of its battle pattern is easy to adapt to. Even easier if you have an electric melee weapon or a water sword to get the missiles without expending energy. Unfortunately I was a glass cannon build. So I ended up cheesing the boss through the semiautomatic doorway.
The Floran party I actually found kinda fun. Platforming, grapple gun exploration, very fun traps (to avoid). Remember to bring grapple guns and antitoxins though. A shield and a one-handed ranged weapon of some kind are also a must.
Maybe I'm just too fond of classic Nintendo Hard platformers.
I couldn't get past the first mission. I went in with piles of food, the best weapon and armor I could make, but I got annihilated. Those guys hit for crazy lots of damage and their attacks are almost impossible to avoid. I tried picking them off one at a time from a distance with my composite bow, but then I encountered an enemy who looked like a friend and got killed before I knew what was going on. It took me an HOUR to get that far. I tried a couple more times, but once I realized I'd have to start all over, I started getting very frustrated and eventually just gave up. Which would all be fine if it was optional, but you can't even leave your starting system until you finish that stupid mission. I fully explored all the planets, which were all essentially identical, and didn't find anything better than my craftable equipment. How exactly does anyone beat it, anyway?
I'll be happy if they either make it optional, make it easier, or keep it exactly how it is but SAVE the progress you've made instead of making you do it all from scratch every single time. It takes way too long to get through the dungeon for them to just take back all your progress if you slip up once. That's not a matter of making the game challenging, that's just being dicks to your players.
Sounds like you were terribly unlucky. I was going in with steel armor and at least three different guns. Bring lots of bandages - food is nigh-pointless (if you want to heal slowly there are bunks everywhere), and make sure to bring a shield of some kind. If you can't find a shield, bring a twohanded sword -
anything to block with. Complete the coffee girl's quest and use the tech card to equip Pulse Jump.
Most of all, remember that you don't need to explore the whole facility - just take the shortest path. The infected workers are the worst part of the mission, but there are only what, four of them? They hit crazy hard, but can't jump - all you need is stay out of their way with Pulse Jump, or find high places to stand on and plink away at them.
There's now also a boss at the end of the level, but it's not too hard. Indeed you don't even need any weapons to kill it.
All in all, the mission monsters are only as difficult to kill as the random creatures on the next tier of planets you'll be exploring. Really, if that mission is hard for you, you're not going to have any fun at all at the floran party later.