Hello and welcome to the community!
1.) Yes, this is about as confusing as playing Seiken Densetsu 3 (Secret of Mana 3) where you really need to read over a guide to get a real good understanding.
2.) For the merchant mess, I simply rely on my main "dominant" character. I have him as a warrior mainly to carry the stuff around. Also, in Cyseal, just south of the fletching shop and near the back door to the healing house, there are some crates. Put the real good and expensive weapons in there (for now) to free up some space/encumberance. No npcs should disturb you going into these crates. If one does, have the "side-kick" companion talk to them in a manner that has that NPC facing the opposit direction.
3.)
I'm hoping Larian resolves this issue, it keeps the game from being free-flowing like it should be.
4.) Some common sense actually goes a long way. The electronic machine can't deal with surges of electricity. Fire elementals will be weak to water. Enemies that are wet have a much easier chance of being frozen.
Poison and Fire is a very deadly combination in this game. Fire will cause poisoned areas (or monsters) to explode. Often I find setting the ground on fire and using teleport on a zombie and drop them in the fire to cause insane damage to them. Anything that is a puddle or steam will cause shock damage. You can also cause an explosion by setting an enemy on fire and then casting a poison spell on them.
Your suggestions are said, some already made by others. I'm sure someone from Larian will get to reading them during the week. There is a large update coming very soon that should address a lot of issues with the game. This is forum is also owned by the actual developers, and here they really do read every (constructive) post.
Feel free to ask for help here, there are many that will offer it. We also have some fantastic guides in Help/Tips/Tricks for crafting. Crafting in this game is awesome, but so robust that it is best to use a guide that many people worked on for the past two months.
