In Basketball we have already seen the rise of the Euroleague, which has pretty much become a league of its own.
In football I think there are not enough markets to make the league sufficiently varied (Italy, France, Spain, England, Germany) and on the other hand there'd be too many teams left out.
Therefore I think that CL will become bigger and bigger, but will never "replace" national tournaments, which have far too much prestige.
A merging of national "minor" leagues instead is more likely (see Basketball once again) simply to make them more competitive. Swedish football would gain a lot in a league with Norwegian, Danish and Finnish teams.
Therefore i'd say: Superleague no, but balkan/baltic/nordic leagues probably yes.
Also gotta keep in mind that there's more independent European nations and therefore more national leagues today than back in 1950-1989.
I don't know much about basketball. Portugal is pretty terrible at it. Benfica dominates Portuguese basketball but it certainly isn't top 10 in Europe. It occasionally had good runs in the 90s beating Panathinaikos once even but that's it. Most Portuguese basketball teams are amateurish. And our league seems to mostly buy American player who weren't good enough for the NBA. Portugal is only really good at football and futsal... and roller hockey but only about 3 European countries care about that sport nowadays.
Well yeah several small countries border each other. We don't border any country with a small league. The alternative would be being swollen by La Liga and that would be terrible for us. Benfica and Porto wouldn't want to become an Everton or a Newcastle. I personally would rather be a big fish in a small pond than a small fish in a big pond.