Another update on this for anyone who may be interested.
Well, my 2014 Giant Prime went back to JE James (who in turn I believe returned the bike to Giant to look at). The whole warranty process was incredibly messy, and essentially took a month. The Giant store in Bristol boxed the bike, but did so with the key left in the battery. On arrival at JE James, that key was badly bent. They also lost the second key I'd provided. JE James weren't happy about this, which further complicated things for a day or so.
Anyway, the end result is that I've been provided with a completely new Giant Prime. The one I've been given is the Giant Prime E+ 2 2015 model, which has disc brakes and several other tweaks over the 2014 model. The horrible plastic contraption covering the whole chain/gears etc. isn't on this one. There's no Abus chipSecurity device. The mudguards are made of tougher material and no longer flap around. The wiring looks more secure. The gearshift is much more reliable.
I am no longer experiencing ANY rattle with this model. It seems better put together, and better designed. It looks as though the design update specifically addresses the issues I'd been experiencing (other than the motor cutting out, obviously).
Also, not sure if it's just me but the motor seems somewhat more responsive than the 2014. Not sure whether this is just placebo as I don't have the two to compare. Think the Yamaha motor is the same but there may have been tweaks here?
Anyway, I'm only 2 days into owning the 2015 Prime but SO FAR, I absolutely adore it. It's a fantastic ride, and is everything I'd hoped my original purchase should have been.
Providing the 2015 Prime remains reliable, I'd have no hesitation in recommending it. Fingers crossed.