Layer 3 datacenter interconnects FORCE you to make certain compromises. A given subnet can only exist either on one side or the other. When the datacenter interconnect fails, you can fail an entire network over, or not. Now, L2 is simple, but can cause some serious issues when it comes to performance and troubleshooting as you've basically one or more shared broadcast domains between sites.
So in essence, to give you a short answer: Layer 3 DCI's force you to make design compromises that in the long term will probably result in performance and reliability gains, but these architecture decisions can and probably will lead you to having to do more engineering and architecture.
Each of these decisions need to come for a reason and unless you're having a PROBLEM, I would say why change something that's not broken? You need to define your objectives and reasons for them before engineering a best fit for your organization. A small company with relatively few business dependent DR needs can probably use a L2 connection and some trunked VLANs for some nice simplicity. Someone building a multi-server farm of databases or application servers made available to the Internet and in turn used to RUN the business will have higher requirements.