If there is no 1898 it is unlikley for there to be a WWII down the line.
But alright, Puerto Rico and Cuba were slowly going to be given autonomy by the Spanish government, there plans like that since the 1870s and even by 1898 the conservatives were agreeing with it, especially the moment Cánovas dies/is murdered. As to Philippines, no idea, the Spanish government never cared all that much about them and had them mostly for prestige purposes, Puerto Rico and Cuba were considered as Spanish as the Canary Islands.
Any government that gave in to Cuban independence will be quite tarnished by it. However, in the last elections before the Disaster, in 1898, Puerto Rico and Cuba of the 16 and 30 MPs respectively in the Courts, they returned 13 Autonomists (linked to the Liberals) and 3 Unconditionals (linked to the Conservatives) in PR and Cuba returned 21 MPs from the Autonomist Liberals and 7 from the Cuban Constitutional Union (union of conservatives and anti-autonomy Liberals). Sadly, I don't know if there ever was a large vote rigging in either provinces as it did in the Peninsula, so I couldn't say what was the amount of support they really had, but in any case since 1890 Spain had universal suffrage.
The disaster unleashed a storm of reformist movements, not all of them democratic nor even pacific. There were calls for an end to election rigging and the turno before 1898 and indeed the silvelistas within the Conservatives as well as the Liberal's left were demanding a reform of the system to make not just look democratic but being so. So I suppose reform will be more smoother, and of course, without the disaster there won't be the finger-pointing between government and military leading to the enormous amount of problems Spain suffered in the 20s and 30s.
On the other hand, Spain will remain slightly less developed economically, the return of the Cuban upper classes with their money and knowledge of American new production techniques allowed for some very nice boom years in Spain of fast industrialization beyond Catalonia. Furthermore, it is likely that the Catalan cultural renaissance will continue without developing a strong political side as the Catalan upper bourgeoisie will think that Spain can defend their mercantile and textile interests in Cuba, and they will remain as a Liberal constituency. Meanwhile the Basque bourgeoisie will remain a Carlist or Conservative constituency as Arana's racialist Basquism will not grow beyond Biscay's rural masses and we'll see Basque dying, most likely.