I'm going to pull this since it's clearly an improvement. In the long run, I think things will look something like this:

• We'll expose a low-level app.applytransactions method to all ApplicationTransactions applications (which, increasingly, is "all applications which do anything interesting"). This will be more difficult to use, but give you full control over all possible transaction types and fine-grained validation, error handling, etc.
• We'll retain most of these app.update/app.comment-style single-purpose APIs, but they'll become high-level convenience wrappers for app.applytransactions.

ApplicationTransactions includes sophisticated detection of no-effect updates, including updates which have no effect because they set a value to the current value (e.g., changing status from "Open" to "Open"). This is the real code we should be using to determine that an input has no effect. But we can cross this bridge when we get there.