IMO it was always a silly move to appoint a future Prince of Wales as Patron of the Football Association. I think at the time his team saw it as balanced as he also took of Patronage of Welsh Rugby Union.
Perhaps he should have visibly supported both teams from the off, for example he recently presented England with their shirts… but not Wales.
I think a huge part of the issue Welsh people have (as a half Welshie myself) is generally England is seen as a much better football team (though that is changing) while Wales is seen as on par with England for Rugby. In other words, is he just supporting the ones most likely to win.
It really is just Sport but given the fact they seemed to ensure William spent some times in Wales when he was in RAF it seems odd that in this area they have dropped the ball (excuse the pun) by not thinking it through.
Heck bar the recent loss over Italy I'd say that the Welsh team is better than England!
But I absolutely get what you mean. It would have been easier for William to support either Welsh rugby and football, and for his spouse to support English rugby and football (or vice versa). Though I must say rugby league doesnt have much support in Wales so that may present a problem
IMO it would make sense to have Kate as of the FA (yes I know William was appointed before his marriage) which would allow the Prince of Wales to support all things Welsh.
Though, I must say people may find it weird for William to support Wales and Anne to support Scotland. Neither are Welsh or Scottish (bar some ancestry) and it may appear that they are only supporting the countries because they are obliged to by their position. If they were ordinary Anne and William neither one would probably give Wales or Scotland a second glance.