You can take over the flat is it is completed in all the respects, the other amenities can be dealt with separately.
You are entitled for penal interest at the rate applicable for delay in completion of construction.
The clause that in case of delay caused in getting govt sanctions , builder is not liable.is lopsided and an excuse the bilder can take protection under.
The builder is supposed to get environmental clearance any delay in complying with the conditions laid down to obtain EC shall be the builder's responsibility.
The delay clearly indicates that the builder is intentionally avoiding to comply with the conditions nor he has respect for law.
Only after getting EC, he can apply for OC from the local admin body, it does not mean that he will blame the local admin body for not providing the OC just because he cannot obtain EC and thus escape his liabilities for the delay in completion of construction and handing over the possession or payment of penal interest for this delay.
The builder can very well be dragged to consumer forum for this deficiency, he cannot put forth his argument quoting his lopsided condition mentioned in the sale agreement.
Thus you may first decide based on your immediate necessity and leisurely think about initiating consumer case against the builder by consulting a local lawyer on this