Some items have a red "!" mark on them others have a white "!" on them. Some items have this white X on them and some don't. I can imagine the "!" mark is for story purposes but what about everything else?
The exclamation marks denotes that material or collectible will be used for a quest. Red for a quest you have undertaken and white for a quest you have yet to take. If you are at the point where you have the maximum amount of materials (happened to me after 40-50 hours) or collectibles (that hasn't happened to me yet), then it is probably safe to sort by price and sell a page or so of the lowest valued items.
If you're thinking of selling collectibles, consider using them as gifts between party members to raise affinity. It takes a lot of gifting to raise affinity through collectibles gifting.
Lithium: I feel you on the overwhelming factor. I also don't find the tutorials all that useful. It took a couple of hours of determined trial and error for things to click all the way, as I kept getting my ass kicked by mild groups of same-level enemies. I still don't understand how the gem crafting system works, nor do I understand the skill tree linking thing between characters. I'm hoping I can ignore about 10-20% of the game's complexity and still blunder through (at some point in the future).
I am very familiar with the MMORPG/World of Warcraft combat system that Xenoblade Chronicles is highly reminiscent of. The tutorials made a lot of sense to me when I read them, and I'm sad that I can't imagine how they aren't making sense to you.
Gem crafting isn't immediately obvious, but pretty fun once you get the hang of it. In order to start the process, you need at least two crystals, cylinders, or a combination of them. You don't need to get the qualities to 100% so you can start crafting to generate stronger cylinders. If you do reach or exceed 100% in any quality, then you must start the crafting process.
When you start the crafting process, you will choose one party member to be a shooter and another to be the engineer. The shooter has a character-specific affect to the crafting such as Shulk having a higher chance to go in to a crafting fever or Reyn generating higher percentage gains when the engineer produces a strong flame. The engineer produces one of three flames (strong, medium, and gentle) during a turn. The descriptors of "Strong Flame: average" and "medium flame: good" refer to the odds of that particular flame being used for a crafting turn. For example, Reyn as an engineer is great in strong flames and poor in medium and gentle flames. That means he is more likely to produce a strong flame for a crafting turn than a medium or gentle flame.
Once you select a shooter and engineer, the crafting process essentially turns in to a gambling machine as you watch the gem qualities or green cylinder rise. How many crafting turns you get depend on the affinity level (yellow, green, blue, purple, magenta) between the shooter and the engineer. At the maximum affinity level, a pair can have 10-15 crafting turns.
What happens during the crafting turn:
The shooter will shoot... something in to the furnace and the engineer will produce a flame.
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strong flame will greatly raise the percentage of one gem quality. This is very useful in pushing a quality over 100% (where it will produce a gem), 200% HEAT, (where it will produce a gem one rank higher than the materials your are using), and 300% MEGA HEAT (where it will produce two gems that are one rank higher). The strategy to take advantage of the strong flame is to select materials in an order that will get gem qualities as close to 200% as possible, to have as few gem qualities being crafted as possible, and to have a crafting pair that will raise the percentages the highest (this pair is Reyn's Strong Bonus and Dunban's Strong Flame: Good).
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medium flame will raise the percentages of all gem qualities. The percentage gains aren't as high as with a strong flame, but you do have the medium flame raising the percentage of all qualities in the mix.
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gentle flame raises the green cylinder gauge located to the right of the gem quality readout. At the start of the crafting process, the cylinder gauge result with be at one. The number represents the number of cylinders you can create out of gem qualities that failed to reach 100% or higher at the end of the crafting process. If a gentle flame is produced by the engineer, the cylinder gauge will rise and eventually increase the result. Normally, you wouldn't worry about this number since you should only be crafting two or three qualities at a time, but it is a number to look out for if you plan on creating a lot of big cylinders in one go.
During crafting, the pair may go in to a fever state where one turn becomes many shots. It happens at random, but you can increase the chance by having Shulk be the shooter or raising one of Shulk's skill tree to an "All" skill that increase the fever chance. If you have increase the affinity of the entire party to each other, they may randomly support the crafting pair with an extra turn.
There's a lot more to the crafting than this. Play around and go for those HEATs! One strategy you can employ is to create high quality cylinders with Melia and Sharla or Sharla and Riki. Then you can use Reyn and Dunban to craft those cylinders to hit HEATs or MEGA HEATs.
Skill linking is comparatively simple. Skill links allow party members to share skills. The number and types of skills allowed is determined by the affinity level between two party members. Higher affinity levels increase the number and type of slots available in a skill link. For example, Reyn has the Heavy Armor skill with a sun-shaped slot early in one of his skill trees. When Reyn has acquired that skill, he can link that skill to another party member who has reached the affinity level with Reyn to have an open sun slot. Shulk opens a sun slot early in his skill link tree with Reyn. Now you can use thirty affinity coins to have Shulk be able to wear heavy armor, something he can't do in his own skill trees.
Ah, affinity coins. You earn those for your party by leveling up and defeating unique monsters. You use affinity coins to set skill links. Those coins are fully refunded when you remove a skill link so don't be afraid to mix and match skill links. For each party member, there is a separate skill link tree per every other party member. It is best to think of skill linking as having an additional 2 or more skill trees to a character's regular three.
Get more party members, raise everyone's skills, raise everyone's affinity between each other, and then you will have a huge pool of skills choose from.
*Side note about a character's regular skill trees.*
All acquired skills are always active for a character. Acquiring Reyn's Heavy Armor skill in one tree and then switching to a different active tree won't deactivate Heavy Armor. What is getting activated and deactivated? Each of the three skill trees has a passive bonus such as +10 to Strength or +3% to Critical Rate. That passive bonus is what is being activated and deactivated for a character. You will notice later in the game that your maxed strength skill tree gives +50 to strength while the agility skill tree you're thinking of switching to only has a +10 to agility. Do not despair! Getting more skills is more important. Also, the passive bonus of a skill tree increases as you acquire more skills in the active tree. Worry about which passive bonus to have active after you have acquired all of a character's skills.
EDIT: I think may have wrote too much. Ah....