I disagree on plan and todo-list, which seem relatively not needed to me. No comment on goals/looping, which I don't have much experience with.
To me it's great how minimal the system prompt and tool set is, and I doubt those features are worth the tokens for every model. (Who knows if they improve performance for SOTA models, and they probably harm performance for small local models.)
I would add "better sandbox" support, which I think should be included out of the box. Not having a very simple way to get out of "yolo" mode is kinda crazy. Sure, there are plugins, but they do have some issues.
pi-bash-approval is good, but manual approval plus allowlist is a "bad" way to run coding agents.
The "best" way in my current opinion, is where commands run by default in a sandbox, but commands can be ran unsandboxed as needed, requiring approval or allow-list in that case. Cursor was pretty good at this (when I used it). For example I don't want to configure my sandbox with access to docker, which would present easy jailbreaks, but I do want to allowlist certain docker commands or approve them to run on my host as needed. pi-sandbox is good at allowing me to configure sandbox access, but this feature where somethings can run unsandboxed is missing. I write more about this and about (hacky, but productive enough) workaround here: https://github.com/carderne/pi-sandbox/issues/50
the thing is about some of these things, like sub-agents, is that any implementation of sub-agents is going to be extremely opinionated, so it would never make sense to be in pi out of the box.