Aha! so glad as I was hoping you would see it that way instead of intrusive.
How the chains grow. The super-heat (Obviously not affecting his body etc) and literally melt to molten metal and drip either onto the floor or something similar and then start to cool down revealing they are now chains. When I said shadow below you I was imagining when you use your shadow step ability the chains (after wrapping around you) melt again and drip onto the floor turning that black to, into a shadow into which you disappear.
The shadow-stepping I have no problem with, I assume it's like Koryaku's ability? but as you say you can't step into opponents shadows which is a limit I really like.
Finally I would never think the idea I put forward are better than your own, it's all down to a sense of personal style and I suggested what I would think would be really cool. I'm happy you like them, and if you choose to use them that will be awesome. But your style might be different to mine, which is completely fine and awesome. and far be it from me to push my ideas on others.
Edit:I've never actually played Prototype but I see what you mean. I've suggested some ideas for you Shikai but I think it might be going to far to do the same for your Bankai, I'm willing to help just send me a PM or hit me up on Skype. But please don't think you have to ask my opinion on everything, your definitely capable of making up some cool shiz on your own, so only ask if you actually need help dude :D
Second Edit:So I'm going to throw up what I'm thinking will be Nobunaga's Zanpakuto. It's only rough and it's not fully explained but it should give you all an idea of what he is capable of. Feel free to throw out suggestions and amendments to it, or if you had a completely different idea for his Zanpakuto please share :D
Shikai: Sorasu, Renkinjutsushi (Bend, Alchemist) (Ren-kin-jut-soo-shi)
Shikai Abilities: Renkinjutsushi's Shikai ability is to materialize or create Electrons and force them to bond with Atoms changing an elements electrical charge. Nobunaga can charge the atoms around his sword easily, an object he stabs charges and effects the entirety of its physical boundaries. Renkinjutsushi can also target a specific area in an object to charge. For instance, one of his favorite techniques is when his blade makes contact with another he will charge the fluid used for balance encased in the inner ear. This means all the atoms in the fluid begin to repel each other, causing violent flow as it tries to expand. As well as causing pain, this leaves the opponent completely off balance until the effect stops, when Renkinjutsushi is sealed again.
Bankai Abilities: Nobunaga's Bankai is a step above his Shikai, as well as letting him create Electrons he can now create Protons and Neutrons meaning he can change the atomic number of an atom completely changing it's element. This ability is bound by the same restrictions his Shikai is, meaning his sword must touch the object or a connecting object to his target.