That can indeed be done, although I fear that many clients and servers would implement these additional features differently, thus losing all the good that comes from IRC being an open standard.
I don't know if it's been attempted before... but I think it would be interesting to see something open and community-centered like IRC, but with all these little features people now expect.
It might well bee that the best idea going forward is actually to form up a couple of RFCs regarding nickserv and other bots (eg: channel loggers, nickname registration, what are they called, how do they work -- eg: /invite ChanLog -- /who #mychannel -> ChanLog in list -> indicate messages are archived for this channel -- that kind of thing), mandate TLs only connections -- and then have clients implement on top of that.
Perhaps some RFCs dealing with SRV-records (where is the web UI with channel logs?) -- or maybe even RFCs on how to mirror some functions (nickserv, logs) via REST-apis.
I don't know if it's been attempted before... but I think it would be interesting to see something open and community-centered like IRC, but with all these little features people now expect.