Based on the description you provided, there is not much I can propose as it is still all too vague.
Anyhow, it sounds like some sort of semantical pruning would help here.
Have you tried to use the constant-union-filter-approach to enable input source pruning of the different data sources?
As you've had the treat to attend TechED 2015, I recommend to revisit Werner Steyn's session DMM208: New and Best Practices for Data Modeling with SAP HANA | SAP TechEd Online</title></head><body&g… (http://www.sapevents.edgesuite.net/TechEd/TechEd_Vegas2015/pdfs/DMM208.pdf)
Before you ask "why can CE function do that automatically and SQL cannot?": I haven't seen your models, so I really don't know what's happening with those.
Generally speaking, the CE functions cannot do anything "more" or "better" (rather the other way around).
If this doesn't help you all that much, as an SAP employee you always have the option to address this topic internally.
Cheers,
Lars