A few things. In fairness, Ayoob had a very early model in .40 and never went back to re-evaluate after some changes were made, but, I suspect that most of his opinions would remain unchanged. This is a love it or hate it gun.
Yes, the grip is fat, but if you find it comfortable then it's a non-issue as to ergonomics. It remains an issue as to carry, a task that I really don't see the gun to be well suited for. As was pointed out a Taurus PT111 Millennium Pro (or any number of guns) would be a far better choice.
Right out of the box the trigger on this gun sucks. With just a little work that can be fixed. The major issue that I have with the gun is the manual safety. It is way too stiff and requires two handed operation. It has loosened up a good bit, and hopefully that will continue. I may have a smith look at this to see if it can be handled with a lighter spring. Beretta has a tendency to over-spring some of their guns. The slide serrations are very narrow, but in a non-defensive role I can forgive this.
I would opt for the 9mm and avoid the .40. From many opinions that I have read people who have the 9 seem to be far more satisfied. For a self-defense/carry role there are far better guns far better suited for the role. For an inexpensive fun plinker the 9000S has great potential, another good reason to go 9mm. In that role I like mine a lot.
FYI, the gun is now completely discontinued (US and Europe). I was told that by a Beretta tech. He said there are more than enough parts to service this gun for many, many years to come. I have recently seen prices on them go up here locally and they all seem to be .40s. I would agree not to pay more than $300 for one new. If you look at this as a gun that is going to take just a bit of work to get right, there is potential (assuming that you can live with the ergonomics) for a fun shooter. Add to that the 92F mags with the factory adapter and it really makes it a fun plinker, holding 15 rounds.
The fact that Tom Cruise used the 9000S in Minority Report I can't change