Today we have made adjustments to flood controls and further modifications to spam checking. These adjustments work hand in hand. It is often impossible to completely remove spam, so flood control is one method of controlling it.
In general, if you are an Admin, or Sub Admin, of a site then you will notice that flood timers are significantly lower. You probably won't see them anymore, but they do exist for safety. If you are a regular member the flood control is much less. You may still see them, but less. Non-members of sites will see a slightly higher flood control.
In regards to Akismet, we have adjusted when Akismet fires using similar logic as that above. We will be rolling out another update which includes the ability to submit ham and spam to Akismet on a per site basis so the algorithm can be tuned.