Methodologies are pretty good about that in the short term. If Agile were bad at that, then it wouldn't have spread. I think the problem is more Agile in the long term. It's a more general problem faced by longer term software projects.

The answer might be to have shorter term software projects. Make everything more modular, have a standard backplane into which everything can plug into, and enable competing short term projects. I think today's trend is to make corporations into ecosystems, and this change might be able to shape incentives positively.