I dunno, I like this method better really. Having the perk unlocks be attached to relatively simple gameplay tasks rather than arbitrary level locks means you can concentrate on specific skills if you want, rather than having to either sit on your upgrade points for 10+ levels or spread them into dump skills. Gaining XP doesn't seem to be that much slower from other games really, and there are some food items that can raise your XP gain for a while too. It's a lot more engaging than sitting in a corner casting a spell for two hours until you can spend another point of that specific type of magic.
You can unlock a perk that will highlight needed resources on the scanner, though it's a mid-tier option. Since a lot of people don't really bother with making their own upgrades and just use whatever they end up looting, getting stuck into being a full-on crafter is somethng you have to build up towards. The Trade Authority places seem to sell most resources in some quantity too, so that's a (somewhat expensive) option as well.
Generally anything that ends up in the Misc. tab of your inventory is junk and can be safely discarded if you want, something I learned thanks to Fallout 4 conditioning me to obsessively grab every roll of duct tape I could find since they used to be needed for upgrading. It's also noteworthy that when you hover over something that's used for crafting it'll say so in the tooltip description that comes up.
Though on both this and the previous point, something the game doesn't explain to you outright is that you can transfer items from your personal inventory to your ship's cargo at any time from the ship overview, and even craft with or sell stuff right out of the cargo hold without having to transfer it back to your person, so grabbing everything and then sorting through it later is somewhat less of an issue. And considering some of those junk items can be pretty valuable, packratting is still as much of a viable money making option in the early game as it is in any Bethesda game.
