Dungeon Crawl is a great game, and I'm happy to see Whales taking some inspiration from it. It's not like Cataclysm is going to become "Dungeon Crawl: Zombie Stew" Or anything. You're not complaining or anything, are you?
There's a difference between being inspired by another game's style or features, and directly copying mechanics from it. Liking how Crawl does mutations and taking inspiration from that is far different from copying a specific mechanic like "eating mutagenic body parts gives you 1 mutation and using a mutation potion gives you up to 3" and "scale mutations start off generic but then develop into specific colors and styles that grant resistances and properties of their own". It's the difference between inspiration and "inspiration".
Am I complaining? I don't know. I think that it's a pretty bad way to go about development, so I'm mentioning it now before it (potentially) gets out of hand. If you like how another game does something, then consider it, and why it works, and find out how those principles may or may not apply to your own game, then design some implementation that works well for your game. You should never directly copy something from another game just because it works in that game; you should always try to come up with an implementation of your own. I'm probably coming off as a little more harsh than I want to be here, but I figured the game is in early enough development that it's worth discussing these things.
Personally, I'd prefer if the game didn't have these fantasy-style "mutations" at all, and radiation just messed up your body in a more quasi-realistic fashion. We already have bionics for body modification (so the functionality is kind of redundant), and I feel like growing fire-resistant skin or wings because you sat in a pool of nuclear waste just... doesn't really suit this game's genre or style well.
It's hardly like crawl is the only game with mutations in it, and actually, the tree / family system I'm proposing is
entirely different from how crawl does things. Crawl doesn't use a tree; it uses mutation levels. Cataclysm's mutations only have one "level" each, they're an on/off toggle. Crawl doesn't have mutation families. Cataclysm doesn't have mutagenic chunks of meat, and crawl doesn't have mutagenic body parts. Cataclysm had mutations in it well before I'd ever played crawl, and I wasn't aware that crawl had a monopoly on "different types of scales"
I'm not directly copying anything from crawl, I'm creating these things from scratch--to simply see that two games have "mutations" in them and to claim that one copies from the other is slightly absurd. Yes, I mentioned that distilled mutagens might give you up to three mutations. Yes, potions of mutation give you three mutations in Crawl. Does that mean I'm copying from Crawl? Not at all, it's simply convergent design. 2 doesn't seem like enough, 4 seems like too many.
Do I take inspiration from other games? Certainly. You may not know this, but when I started Cataclysm, it was going to be a Left 4 Dead roguelike conversion, in the vein of the popular and excellent DoomRL. I quickly found that I'd created some neat systems for expansive worlds, and decided to take it deeper than Left 4 Dead, while retaining some features from that original vision, most notably the boomer.
Actually, a big theme in Cataclysm is appropriation of elements from pop culture. Triffids, graboids, and CHUDs are all borrowed from classic monster movies. A lot of Lovecraftian monsters are lifted straight from his work. There's tons of Half-Life references in the game. The whole thing is very cinematic; there
is a certain emphasis on realism, but there's also a strong emphasis on realism
within the context of monster/post-apoc media. There's certain tropes in these genres that I adore, however unrealistic they might be, and monstrous mutations are one of them. To say that minor mutations--none are that dramatic, there's certainly no wings--do not fit the genre or style of a game with zombies, giant worms, laser guns, bionics, and subterranean laboratories, makes no sense to me!
On the subject of bionics/mutations being overlapping features, well, I see them as fairly seperate.
Bionics:- Only appear if deliberately installed
- Require skill and strong intelligence to install properly
- Unaffected by any traits
- Are always good, with the exception of a few "failed installations"
- Unlikely to alter playing style dramatically
- Can be activated on demand
- Usually require power to use, meaning the player needs to seek out their power source
- Often impact the player's skills, HP, pain, & other numbers, with a weak or non-existant impact on game mechanics
Mutations:- Can be deliberately induced, or may appear from a wide range of sources beyond the player's control
- Unaffected by skills or stats
- Affected by the "Robust Genetics" trait
- Can be good or bad
- Can alter the player's routine or playing style dramatically
- "Always on," no mutations can be "activated"
- Similarly, do not require any kind of power
- Have limited impact on skills, HP, pain, etc., but a stronger impact on basic mechanics
Not really that much overlap between the two, honestly.