Portuguese here! 
I’m sorry, this is going to be a long reply… 
Your style seems to me very modern and international when it comes to boys names, but very traditional Portuguese and old-fashioned when it comes to girls names.
[name_f]Indigo[/name_f], [name_m]Atlas[/name_m] and [name_m]Osiris[/name_m] are unique and adventurous. I think they work well in multiple languages. I also really like [name_m]Cosmo[/name_m]! It is on my list. Jaime’s pronounciation in [name_f]English[/name_f] and Portuguese is quite different, for example, and based on what you said, I think that will bother you. Unfortunately, most J names are difficult to use in these two languages. Of course, that may not be a question if you are considering moving to a country that speaks another language.
I adore Romeu! What about the spelling [name_m]Romeo[/name_m]? It looks more international. It is used in Romanian, [name_f]English[/name_f] and Italian. I think it is used in some Spanish-speaking countries too!
I think both [name_m]Malakai[/name_m] and [name_m]Malachi[/name_m] are allowed in Portugal, nowadays. The law says that even when the baby is born in Portugal and their parents are two Portuguese citizens, as long as there is another Portuguese person in the world with that name, the name will be accepted for everyone who wishes to register it.
I don’t know where you live, but in my area, a big percentage of the babies born nowadays are sons and daughters of immigrants. I frequently see babies named [name_m]Apollo[/name_m], [name_m]Luan[/name_m], [name_f]Sophia[/name_f], [name_m]Ravi[/name_m], [name_f]Athena[/name_f], [name_f]Kelly[/name_f], [name_m]Bryan[/name_m], [name_f]Yana[/name_f], [name_m]Gael[/name_m], [name_f]Mayara[/name_f], [name_m]Tymofiy[/name_m], [name_m]Diego[/name_m], [name_f]Ayla[/name_f], [name_m]Matteo[/name_m], [name_f]Deisy[/name_f], [name_f]Aisha[/name_f] and [name_m]Enzo[/name_m], for example. I can see [name_m]Malakai[/name_m] being used in Portugal, but [name_m]Malachi[/name_m] will be mispronounced a lot, I’m afraid.
[name_f]Sancha[/name_f] and Mercês are very traditional names, but they were forgotten in time and disappeared after the end of the monarchy, from my perspective. At least, I’ve never met anyone with those names and I work with dozens of people of different ages every week. I see the characteristics that they share with some popular choices like [name_f]Aurora[/name_f], [name_f]Madalena[/name_f], [name_f]Benedita[/name_f], [name_f]Matilde[/name_f] and [name_f]Leonor[/name_f]. However, I don’t see [name_f]Sancha[/name_f] and Merces returning to the spotlight. Perhaps they will reappear in some more traditional families and religious areas, but not at a national level. I can be absolutely wrong, of course. All it takes is a famous artist or character appearing on TV for the situation to change.
Some names that I see gaining popularity are [name_f]Teresa[/name_f], [name_f]Cecilia[/name_f], [name_f]Emilia[/name_f], [name_f]Penelope[/name_f], [name_f]Helena[/name_f], [name_f]Teodora[/name_f], [name_f]Eduarda[/name_f], [name_f]Amelia[/name_f], [name_f]Manuela[/name_f], [name_f]Julia[/name_f], [name_f]Eliza[/name_f] / [name_f]Elisa[/name_f], [name_f]Heloisa[/name_f] / [name_f]Eloisa[/name_f] and [name_f]Celeste[/name_f]. Basically, traditional underused Portuguese names or Portuguese variants of names that are popular in other countries like [name_m]Brazil[/name_m], UK, Spain, [name_f]France[/name_f] or USA.
Caliope, [name_f]Julieta[/name_f] and [name_f]Arabela[/name_f] are amazing! I think they sound wonderful with [name_f]Indigo[/name_f] and [name_m]Atlas[/name_m].
[name_f]Clotilde[/name_f] may be usable outside Portugal because it sounds like a mix of [name_f]Chloé[/name_f] and Matilde/Matilda. However, I’m not the best person to answer to that. Similar to [name_f]Jorja[/name_f], you may also consider [name_f]Georgia[/name_f], [name_f]Georgina[/name_f] or [name_f]Georgiana[/name_f]. I think all the 4 options are good alternatives for you.
I don’t know were you are considering to live abroad. That may affect in many different ways the perception and usability of your favorite names.
Names recommendations for you:
Boys names
[name_m]Victor[/name_m]
[name_m]Helio[/name_m] or [name_m]Elio[/name_m]
[name_m]Augusto[/name_m] or [name_m]Augustus[/name_m]
[name_m]Samuel[/name_m]
[name_m]Antonio[/name_m]
[name_m]Clemente[/name_m]
[name_m]Ismael[/name_m]
[name_m]Maximo[/name_m]
[name_m]Nico[/name_m]
[name_m]Santiago[/name_m]
[name_m]Jorge[/name_m]
[name_m]Luciano[/name_m]
[name_m]Gabriel[/name_m]
[name_m]Mario[/name_m]
[name_m]Adrian[/name_m]
[name_m]Valentino[/name_m]
[name_m]Delfino[/name_m]
[name_m]Ruben[/name_m]
[name_m]Sabino[/name_m]
[name_m]Orlando[/name_m]
[name_m]Igor[/name_m]
[name_m]Joel[/name_m]
[name_m]Marco[/name_m] or [name_m]Marcos[/name_m] or [name_m]Marcus[/name_m]
[name_m]Baltazar[/name_m]
[name_m]Cassio[/name_m]
[name_m]Edgar[/name_m]
Avelino
[name_m]Hugo[/name_m]
[name_m]Ciro[/name_m]
[name_m]Oscar[/name_m]
[name_m]Tobias[/name_m]
[name_m]Julian[/name_m] or [name_m]Juliano[/name_m]
[name_m]Martin[/name_m]
[name_m]Alexandre[/name_m]
[name_m]Maximilian[/name_m]
[name_m]Emilio[/name_m]
[name_m]Isidoro[/name_m]
[name_f]Rio[/name_f]
[name_m]Amadeus[/name_m]
[name_m]Camilo[/name_m]
[name_m]Daniel[/name_m] or [name_m]Danilo[/name_m]
[name_m]Elias[/name_m]
[name_m]Cruz[/name_m]
[name_m]Ivan[/name_m]
[name_m]Marcel[/name_m]
[name_f]Azul[/name_f]
[name_m]Lino[/name_m]
[name_m]Angelo[/name_m]
[name_m]David[/name_m]
[name_m]Manuel[/name_m] or [name_m]Emanuel[/name_m]
[name_m]Felix[/name_m]
[name_m]Nestor[/name_m]
[name_m]Octavio[/name_m]
[name_m]Rafael[/name_m]
[name_m]Sol[/name_m]
[name_m]Adonis[/name_m]
[name_m]Dario[/name_m]
Arthur/Artur
[name_m]Silvio[/name_m]
Girls names
[name_f]Susana[/name_f]
[name_f]Luisa[/name_f]
[name_f]Irene[/name_f]
[name_f]Eva[/name_f] or [name_f]Evelina[/name_f]
[name_f]Felicia[/name_f]
[name_f]Celina[/name_f]
[name_f]Jordana[/name_f]
[name_f]Delfina[/name_f]
[name_f]Amara[/name_f]
[name_f]Rosalia[/name_f]
[name_f]Bia[/name_f] or [name_f]Bea[/name_f]
[name_f]Lidia[/name_f]
[name_f]Lourdes[/name_f]
[name_f]Elsa[/name_f]
[name_f]Miriam[/name_f]
[name_f]Larissa[/name_f] or [name_f]Lara[/name_f]
[name_f]Adelaide[/name_f] or [name_f]Adelina[/name_f]
[name_f]Barbara[/name_f]
[name_f]Paula[/name_f]
[name_f]Cassia[/name_f] or [name_f]Cassandra[/name_f]
[name_f]Amalia[/name_f]
[name_f]Isadora[/name_f]
[name_f]Simone[/name_f]
[name_f]Josefina[/name_f] or [name_f]Josefa[/name_f]
[name_f]Vera[/name_f]
[name_f]Dina[/name_f]
[name_f]Isabel[/name_f]
[name_f]Filomena[/name_f]
[name_f]Tania[/name_f] or [name_f]Tatiana[/name_f]
[name_f]Noemi[/name_f]
[name_f]Olga[/name_f]
[name_f]Regina[/name_f]
[name_f]Telma[/name_f]
[name_f]Amora[/name_f]
[name_f]Laura[/name_f]
Betania
[name_f]Cristina[/name_f] or [name_f]Cristiana[/name_f]
[name_f]Dalia[/name_f]
[name_f]Estela[/name_f]
[name_f]Leonora[/name_f] or [name_f]Leona[/name_f]
[name_f]Anabela[/name_f]
[name_f]Vanessa[/name_f]
[name_f]Otilia[/name_f]
[name_f]Flora[/name_f]
[name_f]Adriana[/name_f]
[name_f]Diana[/name_f]
[name_f]Elizabete[/name_f]
[name_f]Lucinda[/name_f]
[name_f]Gloria[/name_f]
[name_f]Olinda[/name_f]
[name_f]Marta[/name_f] or [name_f]Martina[/name_f]
[name_f]Luana[/name_f]
[name_f]Flavia[/name_f]
[name_f]Aline[/name_f]
[name_f]Vivian[/name_f]
[name_f]Gaia[/name_f]
[name_f]Augusta[/name_f]
[name_f]Eliana[/name_f] or [name_f]Eliane[/name_f]
[name_f]Veronica[/name_f]
[name_f]Dulce[/name_f]
[name_f]Clarisse[/name_f]
[name_f]Lena[/name_f]
[name_f]Alexandra[/name_f] or [name_f]Alexandrina[/name_f]
[name_f]Natalia[/name_f]
[name_f]Dora[/name_f]
[name_f]Magda[/name_f]
[name_f]Liana[/name_f]
[name_f]Helga[/name_f]
[name_f]Apolonia[/name_f]
[name_f]Bianca[/name_f]
[name_f]Mara[/name_f]
[name_f]Calista[/name_f]
[name_f]Rosa[/name_f]
[name_f]Natasha[/name_f]
[name_f]Ingrid[/name_f]
[name_f]Anita[/name_f]