What have you experienced, I have installed a few and other then transformer loads which I just use a delayed contactor on them I haven't had any problem with them in any other areas, other then the PITA of having to get the start up code to get it to run for the first time which installers who would not fill out the warranty card and send it in brought that on, and also it does some what deters theft as if some one steals it and you report it to Generac they can track down anyone trying to get the code again unless they are after just the scrap prices.
The oldest unit I installed with a Nexus controller was installed in 2008 and have not had one bit of problems with it?
Older units had problems with the batteries as they still were trying to use a trickle charger which does not shut off after the battery reaches float voltage and this had the effect of causing it to loose water which if it was allowed to run dry can cause a battery explosion, the problem was their engineers didn't think about the problem that we could no longer find maintenance type batteries that had removable fill caps that would allow the battery to be maintained, but after I wrote a lengthy letter to one of their engineers, they changed to float type chargers that shut off when float voltage is reached (14.2v) so maintenance free type batteries work just fine, when the Nexus controller was developed the battery charger was included on the mother board so no more trying to figure out where to put the wall wart charger.
I will agree that their alternators do not like to be over loaded for very many times, I have lost 3 alternators where in one case the home owner took it upon himself to add a hot tub that put the load just over the rating of the generator, he said it tripped the breaker on the generator just fine but after about 4 or 5 times the alternator lost one of the hots, in the windings, another case was an old 5kw unit that the owner kept connecting more loads to it till it smoked the alternator, so I can't totally blame Generac for it, but it still should not have burned up the alternator with the breaker protecting it working correctly, they handle bolted faults just fine as the breaker opens faster, but overloads that are right at the limit of the breaker are the ones that get the alternator as the breaker might hold for hours.