Is Neovim flexible enough that it could stop being vim? Remove the modal key-system and implement something of your own? Has enough introspektion to allow something like emacs which-keys? This is a module which show a list of valid keys that can be pressed when you are inside a keychain.
For shell interaction, I use eshell, a UNIX shell written in Elisp, as often as I use anything else. It has some sharp edges, but it takes more sharp edges off shell interaction so it generally makes, for me, the most pleasant way to interact with the shell.
I am aware of no NeoVim project aiming at something like eshell, and it would not, I think, be a good fit for the NeoVim philosophy if it were tried.