2) What are the best mods?
As far as QOL mods go, I quite like Bottleneck (shows whether machines are working, and if not why not, at a glance) and Helmod (production line planner, very useful for getting ratios right). There's also FNEI (which allows you to search items and see what is required to make them), but without a complicated expansion mod everything's relatively simple to keep track of so it's not required, and HandyHands (automatically queues making items on your quickbar), but that easily leads to bad habits. Whatever the mod is that allows you to place things across almost the entire screen is also popular, but I find it too much like cheating for my liking, along with Squeak Through (allows you to move between buildings you normally can't), but I haven't found that too bad.
If you were looking for something to make the game more complicated (which I wouldn't advise until you are very comfortable with the vanilla stuff), then there are three main mod sets: Angel's mods, Bob's mods, and Pyanodon's mods. Each are a set of mods each made by the same person, not just a single mod, so you can leave out specific bits you don't like.
Angel's and Bob's mods are frequently used together (and are afaik designed to be at this point), with Bob's adding complexity in intermediary and finished products (including adding a bunch more tiers of assemblers, belts, and modules, with the higher tier modules being OP to the point of having an option to disable them) and Angel's adding complexity in the ore to plate chain, with completely redone ores which each can be refined into up to 5 or 6 types of plate each (with a lot of overlap).
Pyanodon's mods I have very little experience with, but they are not compatible with either of the other sets as far as I am aware, but doing similar things in a different way.
There are also a lot of other useful mods, but almost all of those are probably best found by asking yourself which parts of the game you want some sort of help with and then doing some more targeted research (for example, if you want laying long sections of rail track to be easier then look into FARL).
3) The bugs seem a bit too docile. and the resources a bit too convenient. Does it ramp up in difficulty, and does everyone have their own preferred map gen tweaks?
The bugs do get harder as time and progression go on. There's a hidden "evolution factor" that increases with time, pollution being absorbed by spawners, and spawner kills that makes the spawners start making higher tiers of enemies, and as your factory gets bigger you'll make more and more pollution, which will eventually reach spawners which will make more and more bugs, The attacks can still be mostly circumvented by preemptively attacking spawners that are near your pollution cloud, but by doing so you'll still be increasing the evolution and they'll also slowly spread back into the cleared area. All of that said they are designed to be a problem of making sure you have the capability to repel attacks set up than an existential threat, so it usually takes a few things going wrong in a row to cause significant damage to a factory and losing an entire game to them is relatively rare (unless you turn the settings way up).
You can try turning the resource settings down (if you aren't already using the 0.17 experimental versions then that has changed how the sliders work to be properly independent of each other), and if that doesn't give the results you want then look into Resource Spawner Overhaul which changes the distribution method, has a much sparser default setting, and allows better fine tuning.