AWS introduced API Gateway because they want back-ends being built on AWS Lambda. They will raise the limits, but this is all bleeding-edge tech and they are likely moving forward with caution.
We'd like the "Total size of all the deployment packages that can be uploaded per account" increased. Since you have to "require in" (as you put it) all your dependencies with each published function it's plausible to hit that limit pretty quick.
The average node module is 1.6MB [2]. If your functions have 3 dependencies, you're near 5MB. That limits you to ~300 functions. That initially seems like a lot until you realize you may have to start breaking up complex logic into multiple functions to hit time limits. You also might need to maintain multiple versions for backwards compatibility (think v1 endpoints). And if you use Java 8, you're just screwed. That size limit can be hit quick.
[1] - https://web.archive.org/web/20150315092544/http://docs.aws.a...
I could also see Lambda adding a paid-for option to keep a function "warmed up" at all times.
It's going to get crazy up in here...