I’m a sucker for crafting and breeding systems that allow you to customise equipment and/or characters. But it’s really hard to find good implementations of the idea, most have some obvious flaw:

• Pokémon (breeding) - in early games RNG plays too much of a role, so it’s hard to get what you want. Late games don’t fix this, instead they allow you to skip the process altogether (see: hyper training).
• Niche - the breeding part of the game is actually really good, a shame that the rest of the game is a slop. For example gathering food gets a PITA once you got too many nichelings, and yet you want them to support your breeding pairs.
• RimWorld (Biotech; germline genes) - arbitrary restrictions that must be lifted through the usage of mods.
• RimWorld (crafting) - now we’re talking. If you pay close attention to which materials you’re using for which tasks, it pays off in the long run. There’s some luck involved, but you can get perfect (legendary) stuff fairly often if you know what you’re doing.
• Leaf Blower Revolution (leaf crafting) - the game encourages you to craft a lot of leaves and salvage most of them. That’s fine, it’s easy to get cheese anyway. The problem is the sheer amount of beer that you need to get the properties that you want in each leaf.
• Monster Breeder (old Flash game) - the game is a bugfest, and the lack of any sorting system makes you have a hard time even knowing which monster you should be breeding with which.
• Minecraft (tools and weapons) - vanilla has a really dumb system that doesn’t fit well in a game that encourages hoarding piles of materials into chests. The mod Tinkers’ Construct fixes this, and makes the system next to ideal.

Plus a lot more that I didn’t mention. Sorry for the wall of text.