إِنَّ الْمُؤْمِنِينَ إِخْوَةٌ
Certainly the believers are brothers.
إِنَّمَا الْمُؤْمِنُونَ إِخْوَةٌ
The believers are indeed brothers to one another.
In the first construction “inna” governs its accusative noun and nominative predicate. In the second “innamā” expresses restriction and “al-muʾminūn” remains nominative as a subject. This demonstrates why emphasis, restriction and case assignment must be separately analyzed.
The first is a constructed grammatical comparison; the second is the selected Quranic wording.