As some have said in previous posts, a second Spanish leader might seem a re-skin to many.
However, I think there are deeper reasons why Spain gets so little recognition in Civ4 (and elsewhere).
Spanish eclectic history swings from being extremely dominant to being extremely dominated. At the crossroads of Africa and Europe, as well as at the crossroads of the Mediterranean and the Atlantic, Spain is uniquely posed to be the ideal conqueror and the ideal conquered, and it has been both, so many times. Spain was been partially or totally occupied many times (Celts, Phoenicians, Greeks, Carthaginians, Romans, Goths, Vandals, Suebi, Alans, Muslims, English, French, etc.) and it has held positions around the world (the Netherlands, Austria, Northern Italy, the Spanish Main, a large part of South America, a large part of North America, parts of Africa, the Philippines, Taiwan, etc.)
Think of any civ and if they have not threatened Spain, then probably the Spaniards have found some way to mess with them (the only exception in civ4 would be the Mesopotamian civs, I’d say). It was the Spanish Legions at the Catalaunian Fields along the Romans who defeated the Huns.
Spain has also swung from extremely backwards and regressive (legendary religious intransigence, political corruption, they even coined the saying “let them [foreign nations] invent [rather than us]” and “Spain is different [for not being a democracy in the 1970s]”
to extremely innovative and daring (leading in conceiving the modern nation-state under the Catholic Monarchs, leading in experimenting with anarchy during the Spanish Civil War, both the debate on slavery and the development of monetary theory by the scholastics of the School of Salamanca, the development of guerilla warfare during the Napoleonic occupation, etc).
When extremely dominant, which is what we mostly think about when we think of historic Spain, arguably most Spanish leaders might look as clones, in Civ4 terms: Expansive and Spiritual (as Isabella), and one might add Imperialistic.
And this eclipses (in no small part due to the Black Legend) the amazing Cultural significance of Spain: the Siglo de Oro (talk of a Golden Age!), the spread of language and religion through all South America while maintaining a surprising variety of languages and dialects at home, this is the nation of Cervantes, Velazquez, Dali, and Picasso among so many others.
But when extremely dominated, such as under Rome and Islam, Spain has also had an overwhelmingly unrecognized impact. This is a very odd trait and yet quintessential of Spain. Consider this: three great and decisive Roman emperors, Trajan, Adrian, and Theodosius I were from Hispania (The Roman name for Spain). As some scholars have noticed, at that time Rome was more Hispanic than Italic. Likewise, some Spanish Islamic leaders such as Al-Hakam II and Abd-ar-Rahman III who dominated Al-Andalus (the Islamic name for Spain, not just the present-day region of Andalusia) were also great leaders who achieved a remarkable prosperity for Spain while maintaining a staunch independence from other Islamic centers of power.
So to sum it all up, who will notice that Spain is creating amazing works of art in the Golden Century while it is also busy conquering the world? And who will notice that Spain is leading Rome or Islam at a time when it is not visible on the map?