Their marriage was certainly an interesting one. Normally, of course, you would expect that in and medieval marriage the husband would take charge, at least in public. The private sphere could be a very different matter and we have numerous accounts of men and women who had genuinely happy marriages and worked as partners and equals. However, the rules did not really apply to Isabella and Ferdinand, which necessitated a rather different approach.

Fundamentally, Ferdinand came to the marriage in a somewhat weak position. The Crown of Aragon was much smaller both in terms of population and force of arms than Castile. Further, it came with a very weird constitutional system where each of the separate kingdoms retained their distinctive parliaments and privileges against royal tyranny. Getting the constituent kingdoms to actually act in concert was a real issue and hampered the power of the King of Aragon greatly (see Composite Monarchy if you want to know more). Further, Catalan trade was beginning its slow decline which would see it become a very impoverished region by the 18th century. By contrast Castile, despite the withering of royal power under Enrique IV, was still relatively centralised, had a larger population and a much larger tax base on which to draw for war. There were also many fewer institutional constraints on the power of the monarch than in Aragon.

Now that we have set some background we can move on. In many ways their marriage was equal in that their affairs were managed separately in the two kingdoms. This was a personal union not an incorporation of one by another. Both kingdoms retained their separate cortes and even customs barriers. Isabella made sure, for instance, that Catalans were banned from the New World when it was discovered by Columbus. Further, the nobles of both kingdoms were not keen on any integration and tried to keep the affairs of the two kingdoms as far apart as possible, the Aragonese because they feared Castilian despotism and the Castilians because they just didn't like the Aragonese very much.

That said, it does appear as if they were truly a partnership which Ferdinand took a very large share. It was he who took over much of the business of government when his wife was incapacitated with pregnancy, it was he who led their armies into Granada (although she was present) and it was he who took the regency after her death. He also took the lead with taking back royal power in Castile. So while the circumstances of their marriage did not allow him to impose himself on Isabella and she was technically the more powerful I really do think that they worked in concert and relative equality throughout their married life.