For S corporations and partnerships, my interpretation is that the income limit applies at the partner and shareholder level, not the entity level.  I think you'll be able to confirm this to the Form instructions The availability of the credit is reported to the partner / shareholders on the K1 as a separately stated informational item for them to apply the income limit rules.  I also included a footnote to the K1s alerting them to that K1 line item and the income limit. 

I haven't thought about the depreciable basis issue until now - tax credits like this one need to reduce the asset's depreciable basis.  The entity needs to know if the credit will be taken at the individual level.  This would be difficult for an entity with a large number of owners to calculate accurately.  I don't know if this is addressed in any IRS guidance or the form instructions.