Sure, there is no doubt that Castillie came out on top. But this wasn't in a war of conquest, but by political maneuvering that saw the favored Castillie win out in the end.
If you're really picky you could say Aragonese were subjugated through subterfuge and dirty politics, it's not wrong per se, but it wasn't a military conquest by any definition of the term that I'm aware of.
The accumulation of various duchies and counties in the Low Countries under the Burgundian crown in roughly the same timeframe was also done (
mostly) peacefully by political maneuvering. By the same token, the rebellion of those provinces against the heir of the Burgundian crown, Philip II, would be illegal?
Spain wasn't the only such nation, France went through a similar period, but managed to effectively assimilate the minorities to the north and south.
France quite forcefully suppressed expression of regional identity in Britanny, in French Flanders, and most importantly, in the Langue D'Oc.
Germany too was more of a conglomerate of tribes which were kindof similar until late 19th century when national identity arose. Ditto for Italy. Spain is only special in that it unified in a more peaceful way and that the ruling elite bothered far less with integrating its minorities ... or something.
Germany's unification was quite bloodless internally, actually (then I count Austria as "outside"). Italy's as well, Garibaldi managed to conquer Naples and Sicily with 1,000 volunteers. Germany's unification also was done in a federal manner, leaving regional autonomy to the constituent states.
Saying Spain unified peacefully disregards the various civil wars that have been fought throughout the centuries.
These were mistakes, of course. That doesn't mean Catalonia would be best served as an independent state any more than Hesse would be better off alone outside of Germany.
Hesse would be an awkward case, as it would be an enclave fully surrounded by German territory

(did you pick that on purpose?). But what you mentioned in a previous post is spot-on: in a few decades, a split of a state within the EU would be as disruptive as merging two municipalities, i.e., not at all. And I would add: even today, such a split would not have adverse effects on government efficacy when it comes to regions that already have high degrees of autonomy, such as Catalonia, or Scotland, or Flanders, or Wallonia. In fact, they would just cut out the middleman in Madrid, London, or Brussels between their regional government and the European one.
When it comes to independence, I think the overriding principle should be that the state is there to serve the people, and not the people there to serve the state as Frederick the Great of Prussia would have it. When the people want to be independent, let them be; and I agree there with you that that should be a convincing majority, not just barely a majority of 51%.
What Hlafordlaes hasn't mentioned in his posts, is that there was a renewed, increased
autonomy statute for Catalonia agreed in 2006 and that this has been largely struck down in 2010 by the Constitutional Court. That certainly has given a new impetus to a Catalan drive for independence. The Catalans went to the streets with the slogan "we are a nation".
28 years ago, the people of Leipzig went to the street with a similar slogan: "we are the people". There were no deaths, no injuries, there was not even police visible on the street. And that was the oppressive GDR regime.
The Spanish government should also heed Gorbachev's advice to Egon Krenz and his buddies: "He who comes too late is punished by life."