One thing I struggle to get my head around, is the lack of integration with the X9/10.

Yes, those boarding the X11 can buy a ticket which will allow them travel on the X9/10, but it's not the case for those using the X9/10 and wanting to take advantage of the X11. 

How does an ordinary punter standing in Middlesbrough differentiate between the three routes, particularly when they have the same brand-name, are operated by the same company, all go via Gateshead and terminate in Newcastle? 
Never mind that the bus working the X11, may have been on the X9/10 earlier in the week as an allocated spare... 

Surely it is about reducing barriers to public transport, making it attractive and not pi$$ing passengers off to the extent they use the train instead.

As an 'enthusiast', I understand the differences between the three routes. An ordinary punter, the very same punter who GNE want to attract - may not. 
I'd certainly not want to be the driver of an X11 having to break the news to a queue of passengers in Middlesbrough or Peterlee - that their ticket isn't valid, they need to pay a premium or hang-around until the next X10 rocks up.
Even more so, if I then drive off with a half-empty bus, which has struggled to break even on that particular day.

"yes, I do go to Newcastle. Yes, I was driving the X9 just the other day. Yes, it does have the same brand name on the side as the X10. But no, you can't get on the bus unless you pay a premium, even though I'm half empty and there's plenty of seats left'.

*gets back to the depot and chats to colleagues in the canteen*

"mixed bag today, didn't carry many back. Could have boosted numbers with a few Buzzfare pass holders and then taken a handful of cash fares at Boro and Peterlee, but I wasn't allowed. There was a few punters at Washington that had just missed the 4 to Heworth and the X1 to the town. The next buses weren't for another 30mins, but I didn't let them on".

Bonkers.