There's hundreds of reasons why vehicles may be off the road other than requiring repair! Exams have to be done (by law) every 28 days which means everything has to be checked similar to an MOT test, this would take a full day if not more (for prep) so this is why 3963 was painted up as a branded spare.
I'm not denying there are issues with B9s (had one that cut out on the A19 a few weeks ago with steam coming out of the back...) but they're infinitely more reliable than the old B7s were... I'm sure they'll continue to be more reliable when they reach the same age too, albeit obviously not as reliable as they are when brand new.

The coaches were removed from the X9 because of extensive complaints from passengers over the steps, plus of course they weren't wheelchair accessible.
I was one who wanted to see something better than a standard bus on the X9/X10 but there aren't many coaches that meet the same capacity. If you were to use a standard size coach you would have to operate double the mileage by increasing the frequencies to match capacity, which of course involves double the investment not to mention other increased costs (drivers etc).