Learn Arabic (Modern Standard): مسألة الرياضيات صعبة، إلا أن التدريب المكثف ممتاز. - The math problem is difficult, except that the intensive training is excellent.

The connector إلا أن ends with أنّ, which acts exactly like إنّ. This means it requires the noun immediately following it to be in the accusative case (mansub). Therefore, the subject becomes التدريبَ.

Since التدريب is affected by إلا أن, what happens to the adjective المكثف?

An adjective must match the case of the noun it modifies. Because التدريب was forced into the accusative case by the connector, its adjective المكثف must also be accusative.

Why does the word ممتاز remain in the nominative case instead of changing like the words before it?

ممتاز is the predicate (the news or information) of the clause introduced by أنّ. While أنّ changes its subject to the accusative case, its predicate always remains in the default nominative case (marfu).

In the first clause, why is the adjective صعبة feminine singular when it follows the plural word الرياضيات?

صعبة is describing the first word of the idafa structure, مسألة (problem), not الرياضيات (mathematics). Because مسألة is a feminine singular noun, the adjective describing it must also be feminine singular.