Aren't Brazilian Portuguese and Portuguese-Portuguese different to a similar degree that Castillian Spanish and Latin American Spanish are?
It's actually much more similar, even it that seems odd judging from this conversation taking place here. A Spaniard not understanding a Bolivian, for the first time, is normal. Not with the Portuguese-Brazilians. The thing is, Portugal has 10 million people... Brazil 200 million people. And one is a behemoth of a cultural world power and has a share of 1/4 of all fiction in Portuguese TV, not to mention music. While Portugal doesn't export much to Brazil, save a things or two.
Brazilians - from some regions in particular, not Rio de Janeiro or São Paulo, or Santa Catarina, at least usually - are simply not used to the Portuguese accent. But I'm yet to see a Brazilian saying "I really don't get European Portuguese". That is a huge exaggeration, UNLESS we're speaking of some Cockney version of Portuguese (it exists): a New Yorker will simply be unable to understand a working class cockney from London, that's for sure, and same goes for Portuguese.
So, she speaks with a mostly modern accent? I also have a lot of trouble understanding modern Portuguese from Portugal, so I admit that I probably wouldn't know the difference, but I just assumed that they made her with a more historically accurate accent, because Pedro's accent is actually from the 19th century, the kind of accent that I hear in movies set in the Brazilian Empire. Well, Washington's accent doesn't sound historically accurate either, so I guess it could be random
Well, that's no modern accent to be honest... unless you hang around with a terrible kind of Portuguese people eheh. No Portuguese really speaks like her, it's "posh" Portuguese, so that's why it sounds weird to your ears. Even to mine. The Portuguese voice-acting (both for Pedro and Maria) were great, they cared about the accents - the way she speaks is almost a stereotypical account of what you take for the "posh" accent of the Royal Family in Portugal.
Either way, we don't know how were the accents back then... they were (supposedly) closer to the Brazilian (especially Rio) accent though, especially as Maria I ended up living (and dying) in Rio de Janeiro, at the time of her death the capital of Portugal. Either way, I can't believe you don't get what she says - that seems more like cultural conditioning that something else.
All Brazilians I know who play Civ told me she sounds great... so that means they got every single thing she said.
Her accent is a Modern Portuguese, Lisbon-accented, "posh" one (if that's a thing). She uses, though, some archaic Portuguese words mixed in with her posh accent.