When you talk about "single instructions" and "multiple instructions", I don't quite understand what you're saying.
Concerning the second paragraph, it's an open design question. We're doing 128-bit today, because it's useful and widely implementable, and it's a good way to work out the set of operations needed and the semantics. It will certainly be possible to extend the API to 256-bit or even 512-bit or more in the future. However, wider SIMD types either mean that application writers will need to write multiple versions of their code to get portability, or JITs will have to split wider types up on some machines, and while that's doable, it can greatly increase register pressure, so it isn't entirely ideal. Perhaps what we really want, beyond 128-bit, is N-bit, where N is determined by the JIT. Or perhaps we want something else entirely. But it's an open question right now.
Concerning alignment, this is also something that is still an open design question. There are two aspects to it: alignment of the data, and alignment assumptions of the accesses. Alignment of the data certainly matters, but it'll need to be addressed within ArrayBuffer and other places where memory is actually allocated. Alignment assumptions of the accesses are less clearly valuable; if the data is actually aligned, unknown-alignment accesses are just as fast as known-alignment accesses on many processors. And, known-alignment accesses will add complexity in JS engines, as they'd have to handle alignment traps when the data isn't actually aligned. So, it's still being considered.
Memory references via load and store within objects will likely be something we can add once Typed Objects are standardized.
Of course, one can also have SIMD values as properties of normal JS objects or as global or local variables, which you can reference directly without using load/store.
If you have further questions or thoughts on the SIMD.js API itself, you're welcome to file an issue on the GitHub repo issue tracker. Hopefully soon we'll be switching over to a more proper forum, but at the moment the work is largely focused around writing the polyfill code as a reference implementation, so GitHub remains somewhat convenient.