The way I see it all of the advantages are lost except one.
It's more expensive to install and run and more complicated and may be just as noisy.
If you typically sail 50% and motor 50% and catagorize a light electric assist in the sailing side then maybe you can sail 90% and motor 10%.
Lots of if's.
My wife really hates motoring under diesel.
Sorry I'm late to this party, but I thought I'd add my 2c worth based what I've seen - because it doesn't have to be that way:
First off, the system I've seen was: 11kW AC Gen set connected to battery charger and Danfoss Variable Speed Drive (VSD). VSD connected to ABB 3-phase AC electric motor. The batteries where connected into the VSD with automatic changeover to power the VSD off generator if it was running. All off-the-shelf stuff. This system has the following advantages:
1. The gen-set and batteries (as few or many as you want) can be mounted anywhere that's convenient weight-wise - not just in the tail of the boat, but generally somewhere central, under the saloon table for instance - and can be properly sound-proofed since there's no rotating shafts extending outside the box..
2. The gen-set provides AC power to other things in the boat (fridge, hot water, etc.)
3. The gen-set is compartmentalised: Engine-and-generator-in-a-bow. Removal for replacement or serious overhaul is four bolts.
4. The gen-set runs at constant speed, supplying whatever load the engine, batteries, etc. need. Continuous throttle and fwd/reverse is via the VSD.
5. The 3-phase AC electric motor is mounted low in the bilge and takes up hardly any room at all.
With this system, the generator automatically starts only when the batteries are getting low. The owners usually manually run the gen-set when anchoring (to make sure there is plenty of power for the anchor winch as well as the motor) and again during dinner to heat up the hot water for showers and run the microwave - very civilised!
Disadvantages: None I could see - apart from the cost, which may not be all that much more than a conventional set-up if you didn't mind having less batteries and hence running the gen-set more. The various bits do all take up space so it wouldn't suit a small monohull, but on a bigger boat - or a cat - it's ideal.