2 Alezi
Для затравки читаем
это, раздел 8 - "Exception Handling" - там всё написано и написано где есчё посмотреть

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По идее под ответ вам подходит страница 206
Цитата
Internal or External Interrupt Controller
The Nios II IIC is nonvectored, requiring the processor to dispatch ISRs with a
software routine. An EIC, by contrast, can be vectored. With a vectored EIC, such as
the Altera® VIC, ISR dispatch is managed by hardware, eliminating the processing
time required for ISR dispatch, and substantially reducing hardware interrupt
response time.
An EIC has no impact on software exception latency or response time.
Shadow Register Sets
In conjunction with an EIC, shadow register sets speed up hardware interrupt
response by making it unnecessary to save registers on the stack. This feature has no
impact on interrupt latency, but significantly reduces interrupt response time.
Shadow register sets have no impact on software exception response time.
ну и дальше по тексту

Я так понимаю у вас там нет VIC в вашей системе, так ? Засандальте его и померяйте время

по идее должно уменьшится