I've been hearing those "whole house" configurations with small generators will most likely be "outlawed" in the next NEC code cycle (2008).
It seems they think we're incapable of managing loads on our own, and will run each and every light and appliance during an outage. If this trend continues, before long the genset will have to be matched to the service rating... typical 200A service will require a 48Kw genset to be compliant.
All this new requirement is going to do is ensure more jobs won't be filed, and dryer plugs will be used to backfeeed panels.
I too hate the idea of a sub-panel and having to chose what to do with and without... outlets not working, appliances not working, etc. And even with a sub-panel properly configured for an estimated load, the genset can still be overloaded.
Briggs and Stratton has some exciting new products for the home market, like their load management controller - it'll only switch on large loads if there's enough generator capacity to spare, this way critical loads are maintained, and optional loads will come online if available. Best of both worlds.