Some things which would make the favorites list more useful:
Have the Alt+J window look more like the Alt+E window. Channels being grouped by network is more useful than an alphabetical list which ignores the network. It's more useful for the network groups to be an expanded display, so people don't need to double-click on the network name to see their channels.
Have the default be to require a network, as most people aren't in the business of opening a specific channel name at each network they join.
Have a 3rd checkbox in the Alt+J window to choose whether or not to keep sorting the channel list alphabetically. If I want ##mirc to be $chan(1) but it's the next to last of that network's channels in alphabetic order, that means the favorites list can't be used at that network.
Just like the delay before joining channels to ensure nickserv sees your password before you try to join a +R channel, people joining a large number of channels would want a delay between channels to lessen the chance of flooding due to the NAMES keyword and the "/who #channel" replies.
Just has /ignore has $ignore() to return info about the ignore list, /favorites should have $favorites() to return info about that list.
It would need to be clarified whether -a should be used to edit an existing channel, or whether there should be a -e switch. For example, if the only thing that's needed is to change the channel key for an existing entry, without adding the channel if it's not already in the list.