Oddly enough, I read about a third of the BOINC article, and only that article, when I got on their forum earlier today. (Their forum is painfully slow, so I usually only read one or two articles.)
I’ve been running Folding@Home on Windows, Linux, and Mac for several years, and ran it on all my PC’s for a while between SETI classic and BOINC. It is still running on one of my fastest two PC’s at home, and is running on one of the two processors in my Mac. (I have a dual G4, that runs BOINC & F@H. When my new G5 comes in, the two cores will be split this way.) I'm getting very close to 1,000 work units!
If BOINC ever became unstable or had serious issues with all my projects, I’d switch completely to F@H.
There are a few issues. One concern is stability (not just BOINC, but all the shared projects). Another major concern is speed. If you run F@H, that’s usually all you run. For many projects, the work units are released in stages, with successive stages based on the previous results. Since BOINC users tend to run multiple projects, long projects tend to consistently miss the deadlines (think CPN and related projects). I’ve seen “standard” work units take up to eight days on a G4-500MHz processor. The large work units can easily take 4-6 days (sometimes more) on my Intel P4 3.0GHz processor. I’ve never run one of the QMC processes because I’ve only recently had a wintel PC with 1Gb RAM. On my F@H page, it shows number of active processors in last seven and 50 days. The slower processors will sometimes vanish from the seven day count because the work units take 8 or more days (of exclusive 24x7 run time). This is becomming common for my G4.
Anyway, because many of the projects require a steady stream of feedback to progress, if the work units go from two days to a week because they are being shared with an average of three other projects, the F@H projects suddenly can only progress at one fourth the speed.
Another problem is that there are multiple cores. The new Gromac33 is the 8th or 9th core. When you install F@H, you install all the cores.
In a way this last point makes F@H a bit safer, since binary cores, which can be hacked and trojanized, are not transferred. Only data is transferred.
From what I read, it looks like their best option would be to run both clients simultaneously, which would be a pain for tech support. However, this way they can reserve the large and extra large WU’s for their dedicated clients, and have the small and “timeless” WU’s primarily go to BOINC. (The “timeless” WU’s tend to be larger and run longer, but do not have a due date. Users who only fold for a few hours a day are asked to set their system to only get timeless WU’s.)