@Bonkus
Please be more specific on what enemies give you trouble. The enemies you mentioned are totally normal. It's somewhat random who you encounter (zombies especially), and it has nothing to do with your score.
What affects missions in what way:
Score - no influence whatsoever.
Research - unlocks a specific mission, doesn't change difficulty of other missions. These missions are *additional* to the other missions, so if you reasearch them and not do them is the same as if you would just research them later. Most of these missions have no penalty for not doing them. If they have, it is mentioned in the description.
Time - can change the difficulty of some missions. For example mutant progroms can have tougher factions later on, megapol change to plasma weapons at some point. However, most missions have no change in difficulty with passing time. Time also affacts which missions spawn. Easy missions like watchtower and save a sister become rare as time passes, while base attacks become more frequent.
Now some details about the things you mentioned:
Zombies - I assume it's the scientific eperiment mission where you encountered them. And yes, they are a pain and a totally legit reason to gtfo. The real problem of this mission is the Strix zombie and the cryssalid(s), and they will keep beeing a problem for a long time.
Preppers - I assume you mean the prepper bunker mission. These can come with bandits, spartans or zombies. Bandits and spartans should be managable, about the same difficulty as a pogrom. What exactly gives you problems with these? For spartans, the hunting bow with poison arrows is useful. Spartans have kevlar armor that stops bullets, but they have no resistance to poison.
Raiders - They are mutants like your gals and just as sturdy. Armor is high enough that shotguns don't do much damage, so you lack the weaponry to take them down fast. Here, the right tech helps a lot. Again, hunting bows with poison arrows work wonders. A major benefit of the poison arrows is that they have reaction disrupt. That means if they do damage, the target gets drained of tu and is then unable to reaction fire. Beeing able to turn off reaction fire on enemies is really helpful to keep your gals out of harms way.
For tech progression: An important aspect of brainers is that research gives score, and score gives money. In fact, brainers generate roughly as much score/money as their upkeep costs, which means that brainers actually cost *no* upkeep. That beeing said, you should get as many brainers as you have lab space as soon as possible. And then research and build the personal labs.
How fast do you need to research to not get into trouble? Depends on what missions RNG spawns for you. What can end your game is a negative score, or a base assault. Your early melee weapons (+javelins) are strong enough to deal with most things that come knocking at your base, so a base assault will most likely not kill you. Weapon research is not that important.
Negative score is much more dangerous and can be avoided by having many brainers researching things, no matter what they research. They just need to generate score. The RNG part of negative score is the excavator missions, that generate a lot of negative points if you don't see them and deal with them. To prevent this, you need to expand your radar coverage or get enough score from missions and research that you can take a hit.
What to research?
As mentioned, the hunting bow with poison arrows is pretty good and quite essential to deal with raiders. Other than that, I recommend to get bounty hunting as soon as possible. You get extra missions, and the tokens unlock weapons that cover most of your needs. Specifically, the magnum covers all your longrange needs. Confederate gear gives you the electric lasso, which can deal with most armored things you encounter. And you also get the heavy pistol, which is very similar to a magnum (but not as good at range) in case you don't have these yet.
What also increases your firepower is to get a higher capacity transport. Contacts: car thieves unlocks the blowfish, which is slower than the airbus but carries 8 instead of 6. But here the right time to research depends on your financial situation, since the research is useless if you don't have the cash to buy the craft. Same goes for overcharged radar.
To make more money, chateau and gambling are the important techs. Once you have chateau researched and have enough apples, get as many runts as you have workshop space. Gambling roughly doubles your money on average if you sell the coupons. If you redeem the coupons that you can, the items you get are worth more (on average) than the coupon itself, and you get a few nice toys here and there.
I also value contacts: smugglers. This unlocks electro flares and cattle prods, as well as seagull missiles.
Edit: I forgot to mention armors. Warrior armor is the fastest significant upgrade, anything substantially better is quite far away (tac armor). Combine the warrior armor with a riot shield or a wheeled machine gun, and you have enough protection from bullets that shotguns pretty much can't damage you.
