We didn't change anything between versions on the service side. In fact, pretty much the exact same service serves both v2.4 and v3, we only use different rendering templates to modify the output of the response to be backwards compatible for v2.4
The other main difference is that the client libraries are quite different.
It might be that you have some default timeout set client side that you need to increase. For example I'm pretty sure this is the case if you use the Java client lib.
-Nick