Let's make as many countries have alternate capitals as possible, it shouldn't be too hard, since most territories nowadays are more determined by ethnic groups than be royal houses.
Portugal - Coimbra, I think it was the capital for a time, not sure though
Spain - Toledo
France - Orleans, have Paris be less important of a city and any house which becomes King could move it back to their home. Also Versailles.
UK - York
Ireland - Cork, anywhere really depending on how Ireland is united
Belgium - Liege, perhaps forming from an expansion of the bishopric lands
Netherlands - Amsterdam, no role for The Hague
Germany - literally anywhere
Norway - see post above mine
Sweden - Uppsala, historically most significant city, or build Stockholm in a slightly different place and call it something different
Finland - Turku
Estonia - Pärnu, don't found Talinn
Latvia - probably have to found Riga in a slightly different location and call it something different, its location is too good
Lithuania - have king Gediminas go hunting somewhere else, and you don't found Vilnius
Russia - Novgorod, Tver, Vladimir, or whichever other state unites Russia; or just keep it in Petrograd
Belarus - idk, another vague one where it could be a lot of places, perhaps Polotsk or Pinsk
Ukraine - Chernihiv or another historic principality capital in the country, pretty much the same situation as Russia and Belarus
Moldova - have another city be bigger/more important than Chisinau when Moldova is form
Romania - Alba Iulia, see Zagan's Romania-wank (the original one)
Bulgaria - Tarnovo stays the capital
Greece - Konstantinoupouli of course

or Salonica
Northern Macedonia - Bitola (Monastir)
Albania - Durres; Vlore could work too
Bosnia - Visoko, capital in late 1300's, or Banja Luka depending on how ethnic balance shakes out
Serbia - Kragujevac, see above
Croatia - Perhaps a coastal city like Rijeka or Zadar, also was addressed earlier
Slovenia - Celje, seat of the powerful Counts of Celje, or Maribor, the second-largest city
Hungary - Buda, or Pest
Slovakia - Somewhere further from the border if not united with Czechia, like Kosice
Poland - Krakow, or the Moon
Czechia - Brno if Moravia has greater importance, otherwise Prague seems pretty entrenched
Austria - Graz, if Austria is centered on Styria; Steyr or Linz are pretty central too, but anything after Habsburgs would have to be Vienna
Switzerland - Zurich is a decent candidate
Italy - Turin if S-P Kings decide not to move, or Florence for a similar reason, or Naples if the Two Sicilies unite Italy, or pretty much anywhere else
That should be everyone other than the microstates. Whether you can realistically piece together a history that keeps all of these countries recognizable is another question