On the Eastern half to Cambridge, it was for reasons of capacity and, in any case, the stand time in Bedford made it really feel like two routes anyway.
As for the Western half from Bedford to Oxford, it's perhaps a bit more nuanced. You have a fleet of 64 plate coaches so they're coming up to 7 years old. They've had a few issues in the past anyway with transmissions (I think I heard) but in any case, they're getting on a bit with reliability beginning to decline and replacement is probably due.
So do Stagecoach replace them with a very expensive fleet of new coaches that they may struggle to find a home for in 7 years time and at a time when funds seem a little tighter than in the past and with the uncertainty of what may happen when EWR does appear? OR do they slide across some humdrum but modern and reliable and reasonably comfortable e400mmcs? They've chosen the latter.
I suspect that rather than a withdrawal, you may see the X5 become part of the S5 pattern simply with one bus per hour (or perhaps two) projected eastwards to MK or Bedford
The Elites struggled a lot in several ways on the X5.
Firstly you had problems with using what was effectively a tour coach on a regional express bus service with several bits of "all stops" operation in between, especially through St Neots where in parts it operates the only frequent local service! Gearboxes and door mechanisms didn't like this, strangely enough.
It wasn't helped that originally the route had a dedicated driver pool using tachographs, the route registration was then split to allow use under domestic hours. As a result drivers went from a small group (who understood how to handle the coaches and the technique needed to get the best out of the sometimes clunky Volvo I-shift automated manual transmission) to a large pool of drivers, some of whom thrashed them and didn't treat them gently in the slightest. Holding a I-shift equipped vehicle on an incline with part throttle applied instead of using the handbrake is a surefire way to burn out the clutch, yet such abuse happened more frequently in recent years in my experience.
Secondly the Elites never had the capacity, especially between St Neots and Cambridge. I seem to recall before COVID it wasn't unusual to see a Cambridge or Bedford 'decker (or sometimes even a Dennis Dart!) running a duplicate on some services between Cambridge and Bedford during the peak.
The E400s solved those problems in one swoop. As for toilets, the hotch-potch of Volvo B10M coaches used before the fleet of Plaxton Panthers arrived in 2008 didn't all have toilets fitted, or the "spare" Volvo B7R's that were in use occasionally until fairly recently - the stops at Bedford and Milton Keynes Coachway normally being long enough to nip to the loo if needed.