It's not a secret that Jon and J. Shanks has been the two driven forces behind Bon Jovi in the studio during the latest albums. Even when Richie publicly was Jons right hand, Shanks has always been very close in the creative process.
I guess it comes down to the fact that Shanks knows what Jon wants, which makes Jon feel comfortable. I'd even go as far as saying that Shanks was the one who planted the seed regarding the Killers, U2 guitar sounds that has become more and more present since HAND. For every album it has become less Richie influenced and more Shanks.

So to repeat myself - Shanks delivers what Jon wants in the studio with ease while Phil X is the perfect guy on the road. Like Rdkopper stated, it's pretty much the same situation as Hugh and Alec, except the fact that Shanks actually tours with the band this time. I'm quite sure it will be like this on possible upcoming albums (unless Richie returns). Shanks will be the guitar player, the producer and the co-writer. Honestly, except for Jon himself Shanks is the one closest to Bon Jovi these days.