I just wanted some insight on why after such a grand event that shook up Gangplank, Miss Fortune, and all of Bilgewater, that the Captain Fortune skin wasn't made Miss Fortune's default skin since that is now where she stands in the lore?
Most likely is about resources.
During the Bilgewater event, Riot released the Gangplank update which ended up including what is functionally a Traditional skin.
Having another free skin given during the same event may have been ill-advised, so they released Captain Fortune as a regular skin.
because sex appeal
Because MF is not actually the queen of Bilgewater. Bilgewater is in chaos RN, everyone is trying to get on GP's throne. MF is one of those people.
Because MF is not Captain in the sense of political figure in Bilgewater.
She overthrow Gangplank, but she did not take his place. Actually, no one could. This is why now the city is on civil war.
Just like Tryrant Swain, Queen Ashe and King Trynda. Sure, that skin is canon, but the normal outfits that they use in battle, are the classic ones.
Didn't they say somewhere that her Classic skin is her casual outfit, like when she roams Bilgewater to recruit some people and things like that?
It seems to reflect her appearance for when she hunted GPs men,but she likely changed back to her original design by the time of shadow&fortune.
Because you are greedy and want a free skin.
Because that would be 2 free skins for one event, thats quite of a lot of money they lose, as no other skins would come out that patch. (which is like almost all their revenue for keeping the game up)
I think they wanted to change GP's pic for a long time and this was justa good time
Because, unlike GP, who got a full blown VGU, MF was mainly just her model, which was fine as it is. They saw an opportunity with GP, since his model before was iffy, to do it with a Skin, but MF didn't need a full blown VG.
Didn't she get her VU prior to the Bildgewater event?
If so, it would have been too much work. Captain fortune being her new vanilla skin would have made more thematic sense, certainly, but Captain Fortune is very different from Call Girl Fortune, which would have meant she would need a similar level of work as Captain GP (calling in the VA for separate lines), and all of her skins are built around Call Girl Fortune to begin with. Having them with the serious Captain Fortune VO would probably be considered too jarring.
In other words, thematic consistency took a back seat to logistics.
$
Because Riot knows people will pay for it anyways.
Spirit Guard 
is also his current canon, so.
