I have also reflected on that Queen Silvia "only" received the Order of Isabella the Catholic. She might get another order this time.
I have been thinking about the order Crown Princess Victoria would receive as well, and it seems there is no logic in previous awards. Willem-Alexander was awarded the Order of Isabella the Catholic, but Crown Prince Haakon the Order of Carlos III. Let us see what practice King Felipe will set
The King of Spain actually has several options in terms of orders that are awarded as diplomatic courtesy.
The Golden Fleece is more or less like the Garter in the sense that it should be in theory in the personal gift of the King as a dynastic order. There is some debate on whether that is still strictly true today or not, but, in any case, it is a very exclusive order (currently there are only 17 living members, including 3 members of the Spanish Royal Family) and no one in Sweden is expected to receive it other than King Carl Gustaf, who is already a Knight.
The other orders are civil orders in which, according to the statutes, awards are pre-approved in the Council of Ministers and then made by royal decree on the recommendation of a responsible minister, which I interpret as meaning that they are decided by the government. As diplomatic courtesy, three options are used: the order of Charles III (Carlos III in Spanish), the order of Isabella the Catholic (Isabel la Católica in Spanish) and, as mentioned above but often forgotten, the order of Civil Merit. The collar, both of Charles III and Isabella the Catholic, are reserved normally for Heads of State, whereas consorts normally get the Grand Cross, which, in Spain, is a lower grade. As you have mentioned, some Crown Princes (Willem-Alexander and Philippe) received the order of Isabella the Catholic, whereas others (the Prince of Wales and Haakon) received the order of Charles III, so it is mostly unpredictable. In recent years, the Spanish government even awarded only the
Encomienda de Número of Isabella the Catholic (equivalent to a grade like Knight Commander) to Princess Anne and Prince Andrew, which I find a little bit rude.
If I had to guess, I would say
Queen Silvia: upgraded to the Grand Cross of Charles III;
Victoria and Daniel: Grand Cross of Isabella the Catholic, or Grand Cross of Charles III for Victoria and Grand Cross of Isabella the Catholic for Daniel (the former as for Philippe/Mathilde and the latter as for Haakon/Mette-Marit);
Carl-Philip and Sofia: no Spanish order, or perhaps the Grand Cross of Civil Merit.
I doubt King Felipe has the Order of the Seraphim with the collar. The Order only has one grade Knight/member, but the collar is seen as special distinction to Heads of State. In practice that means fellow monarchs, or the President from Iceland and Finland. As King Felipe already is a Knight of the Order of the Seraphim it's likely that he will receive the collar during this State visit. On the other hand, if was to be made a Knight during this state visit, he would receive the collar during the next Swedish state visit.
The Wikipedia page on "List of Knights of the Seraphim" shows Felipe's coat of arms as Prince of Asturias surrounded by the collar of the Seraphim rather than the grand cross only. However, another page on "List of hono(u)rs of the Spanish royal family by country" lists only Juan Carlos as "Knight with collar", so suppose you are right. In any case, if King Felipe doesn't have the collar yet, it is a good opportunity for him to get it now and even more reason for him to wear it in Sweden.