While they are alternatives rather than upgrades, that really isn't communicated until you go through the grind for them. I started doing a bit of grinding for them because I expected something more akin to an upgrade like is standard in most RPGs, and was thrown off kilter when I managed to get my first one (since I got one core away from crafting one just from random chance in my gameplay, then sat around grinding for a while to try for the last piece). I agree with the balance decision to only have side-grades, but going through that grind process to try and improve your character then just not getting anything if you don't think the side-grade weapon isn't worth using, that feels bad. I feel that if you started the game with one or two sidegrade weapon options either in your inventory or handed to you very early, you'd signpost that that was what you were aiming for and set expectations better. (I don't know if the protagonist carrying around functionally different spare weapons fits with story/character/source material stuff, but you could always just change the item from a weapon upgrade to major weapon mod thingy to explain it a different way instead)
Overkill stuff is an interesting mechanic, but it overemphasizes just gearing into pure damage, then using the resource advantage you build up over alternative options to buy better gem upgrade thingies to make up any stat deficits in other stat areas. It also means any skills you make later that are multi-hit based rather than dealing enough in a single hit to get the overkill threshold isn't really worth using. I'd rather swap out the overkill mechanic for one based on executing low hp enemies with a special skill, so you can try to balance your damage for being only nearly fatal if you want to min-max your drops instead of going balls to the wall damage, and also being able to learn about the mechanic through a skill description rather than being taken by surprise at a random point after you've started playing when you first encounter the overkill mechanic.
Also even if having a large amount of gem shard slots is an interesting way to fiddle with your stats as you go, having to scroll down to see all your inventory slots comes across as clunky menu design.
Anyway, not trying to be mean by being critical here, but these issues are basically from genuinely interesting mechanics just not landing the right way, and seeing someone actually put effort into making an RPG have distinctive gameplay is a great deviation from the standard Hgame schlock around which I really have to praise you on.
Thank you for the quite elaborate review on all this RM!
You're certainly right, and that's a fault on myself for not explaining it within the game. I'll make sure to do so should I use alternative weapons again in the future. Probably would I would do with this system in the future is have the cores not be unique to enemies, and instead have them be universal and allow the player to use them to get specific alternate weapons, maybe some just being straight upgrades but costing more cores. After all, I was experimenting with this idea in the first place, so learning from it was inevitable.
As for Overkill, it's one thing that originally I had removed from the game in early builds, but then brought back at fan request. (As I had used it in my previous game, Agents of P.O.R.N.) Only this time, I tweaked the total health you had to Overkill the enemy by, and changed the rewards you got for doing so. As for the excuting an enemy at low health with a specific skill, that wouldn't fit Makoto's fighting style, which is more akin to just raw overwhelming power, but it's certainly an idea for some future characters to potentially have!
I'll also try my best to include a bit of a tutorial to introduce how Overkill works in my games in future too, thank you for the idea.
I'm guessing you mean the inventory screen for them all and not the equip screen? As I don't think I can change much about the equip screen side of things, but I can certainly look into making the gems stackwithin the inventory, assuming it's possible within RPG Maker MV.
And I know you're not trying to be mean with all these points, you have a valid opinion on the game, and I want to gameplay to be both understandable and fun to play within my games, not just a gallery with a game tacked on