If you're looking for a decent system for "progressing story events", you might try using variables or timers. Fallout 1 had an in-game timer for completing the main mission and if you didn't, you generally lost the game. But, there were ways to extend the time limit so you could level up a bit more, or explore some more. At some point, I think the timer disappears (I've never gotten very far in the game, controls without a manual are too archaic for me to have patience learning at this point) and it lets you accomplish things in a much broader scope as you like, so long as certain mission objectives were completed first. I'm not sure how most players feel about a "timer" for events (as a general rule, most players don't like time limits in games, especially if there's a lot of exploration and such to do), but you could also substitute a simple system that tracks say a variable and certain things you do increase it or lower it, and the higher it gets, the further the story progresses. Though, you'd have to put in "lower limits" so the story couldn't go backwards, ha ha.
Crafting for the sake of crafting bothers me. Here's my issue with crafting most of the time: It's usually wholly unnecessary to the entire game... except for creating the best gear you can obtain. It's typically useless beyond that. Even worse, a lot of what you can craft isn't even a "side-grade" to equipment you can buy or have obtained in a dungeon. Most of the stuff you can craft is basically worthless by the time you can craft it. Or, if it's not, the materials require so much grinding to obtain enough of them, that you've just bogged your game down with unnecessary play times for the sake of "balancing" crafted gear against monster dropped and shop purchased gear. Frankly, I've yet to run into any crafting system I've liked because the gear it creates is either so worthless by the time you can create it to not warrant crafting... or requires so many materials to make that it turns the game into a slog as I kill 100 bunnies for 10 Fluffy Tails that I need to make "Shoes of Lupine Quickness". For me, it just gets ridiculous. Some players enjoy the grind of a video game, I do not. Before I had a job, a social life, bills to pay, chores to do, meals to make, etcetera, I wouldn't have minded a bit of grind in a game (I used to play Runescape, after all), but I just don't have time for that. At least in a Fallout or Elder Scrolls game, I can decide to grind or not to grind. Either play method is valuable in its own way and doesn't really change the difficulty of the game. So, if I have a free Saturday with nothing to do, I might grind out 5 levels in Fallout 4 just for the sake of the Perks. But, if I don't have a free Saturday, I might instead run a few of the main quests or explore a location, then save, and turn my game off, and I'd still have accomplished something that made me of equal power to those Perks.
Things I do like in games... Generally, I like anything that is fully fleshed out and doesn't feel like it's some kind of "brick wall". I also like things that give me options. From MMOs I like clothing and color options (being able to color my armor how I want, as intricately as I want, is something I enjoy). I also like having a lot of build options in MMOs (in general, if there is one "overpowered build" available, or only a couple was to build a class, I don't play that MMO. I want to be how I want to play and still be powerful the way I want to play). From RPGs I generally enjoy battle systems that don't require me to mash attack or the strongest spell/skill I have to win every fight... I'm partial to a little depth in combat. If you have a "on the map" encounter system, I'm partial to what Earthbound did with its system. Enemies run away if you're too strong, or touching them when you're too strong results in an instant-win without having to actually go into battle. I also liked the "can be snuck up on" and "can sneak up on" mechanics in that game as well. I also like the battle systems from Secret of Mana and Secret of Evermore (Evermore had a fantastic magic system I also liked, where you got ingredients and spells could level up as well). Um... I like Job/Class systems, though I haven't seen one done well since Final Fantasy 5... I like being able to customize gear (like say socketing runes or gems or whatever to give added effects), so long as it's not done in the fashion of FFX. I like lots of loot, but I don't like having the vast majority of it being worthless (Borderlands 2 is my example for this... once you have greens, there's no reason to ever look at a white again, because none of them are as powerful or useful as a green... Borderlands 1 did this better, since you always looked over your loot due to the possibility of low tier stuff actually being much better than high tier stuff if the roll went well. Borderlands 2 leads to a lot of loot on the ground that isn't even looked at, which I hate.).
I dunno, I like a lot of different things. Most of what I like, I enjoy because it was executed well at some point and endeared me to it.
All I mean by "don't implement systems for the sake of implementing them" is that you shouldn't put it in because "people think this is fun". You need to include it because it serves a purpose in your game world. A purpose that players will be revisiting or interacting with often, because it is so much a part of that game and not just some random thing tacked on because you thought it needed to be in there since people think it's fun.
I'll use the argument I use against including most mini-games into an RPG as an example. "Oh, sweet, I can play Poker in this Shooter!" "Um... if you wanted to play Poker, why didn't you just save the game and load up your disc of Poker instead?". Kind of understand what I mean now?