Hard to really pinpoint, but its true metal gear has been handled fine since its their bread and butter. But the utter lack of care or frankly anything of their gigantic backlog of IP's being left for dead is one of them. All we see of those franchises is the occasional VC game being released, and nothing more that requires any kind of real effort. And with Lords of shadow 2 doing bad, i cant see them putting any full effort back into that series either. Silent hills is probably down for the count as well with the whole kojima thing and all.
I feel like things have been rather odd behind the scenes there for some time, their E3 2010 press show was kind of the beginning of the end or at least the weirdness
They have so much potential consolewise, but since they can exist with all their other avenues in japan like the slot machines and such, its really been a sad state for most other things they have. First Koji Igarashi left, mainly due to them pushing him aside when lords of shadow came about, and that he had very little budget with the castlevania games he did get to make. And now kojima is leaving, it kind of feels like there are just mismanagements all over the place that arent benefiting them, especially from a PR perspective, which is why they have since added kojima's credits back to all the sites they were removed from. Its kinda like SE with their failure to manage a dev cycle, and sega with its flops here and the eventual step away from console support besides sonic that they are doing now. Im just afraid of what might become of konami if they continue on this trend of bad decisions, which will benefit no one if they just disappear or run MGS into the ground after kojima leaves.