The annoying bit (if I read the OP correctly) is it is now impossible to send all your agents on missions (unless the intel Agents are an a separate mission quota from the nautical ones). If you can only send 1 or 2 or 3 Agents on missions at any time, then having 3 zee captains and 2 spies means idle minions no matter what. Not nice, FBG!
Now, if we have 2 nautical mission slots (and a third which can be purchased), AND 2 espionage mission slots (presumably with a third purchased one, once a third spy Agent is available), then that would be fair.
And if that last was what was meant (and I’ve simply misunderstood), then please disregard this post, and I will refrain from putting so much honey on my breakfast pancakes. 