Forgive my ignorance, but how is Portugal interesting important and unique compared to Spain right next door?
It's not ignorant infact your right, and uniquely enough this EXACT argument was brought up before MTW2 came out and lo and behold Portugal and Spain were pretty darn similiar.

It goes back to history vs unique factions.

Historically CA wants to include the major empires of the era, so while Prussia and Austria (they just seperated) and Spain and Portugal may not have that different units, voices, or geographic regions, the fact is they are rather potent players of the time frame.

Portugal plays a unique role in several wars through this time.

Unlike MTW2 though, I think if CA allows Portugal some of the more gurella warfare units they use later, towards Napolean era, they could be quite unique when compared to the line marching armies of spain.

Just my thoughts.