The first expression that comes to mind is:

Mais c’est comme ça.

e.g.:

Regarde, on a perdu le match, mais c’est comme ça. La seule chose qu’on peut faire, c’est travailler encore plus dur pour le prochain.

Je ne suis pas très fan du nouveau petit ami de ma fille, mais c’est comme ça.

While mais c’est comme ça is relatively close to the English “but it is what it is” but note that its word by word translation c’est ce que c’est wouldn’t work at all in French.

This expression is sometimes used in its “verlan” form (banlieues French, rap lyrics…):

Mais c’est ça comme.

It all depends on the context, but in those two particular cases, believe it or not, a French speaker may actually use “C’est la vie”.

Écoute, on a perdu. C’est la vie. On fera mieux la prochaine fois.

Son nouveau petit ami ne me plaît pas beaucoup, mais que dire ? C’est la vie.

To refer to something that you have to accept even though you may not like it, you can say Il faut faire avec.

• On a perdu le match, mais il faut faire avec.
• Je suis pas très fan de son nouveau copain, mais il faut faire avec.

Note (comment @jlliagre)

One would drop the il in a colloquial conversation (i.e. mais faut faire avec).

I also found this (exclusively for French Canadians)

…c’est ça qui est ça…

Source

https://www.reddit.com/r/French/comments/1zhrhf/cest_quoi_l%C3%A9quivalent_en_fran%C3%A7ais_de_it_is_what/

Further insight

https://oreilletendue.com/2014/04/30/cest-tout-bis/

https://www.wikebec.org/cest-ca-qui-est-ca/definition/

You could try voilà or bon

Look, we lost the game, but it is what it is.

Écoute, on a perdu le match et voilà.

I’m not terribly fond of my daughter’s new boyfriend, but it is what it is.

Je ne suis pas un grand fan du copain de ma fille mais bon.

One idiomatic way to express it, albeit not formal at all, would be :

C’est l’jeu, ma pauv’ Lucette.

This come from a TV advertisement for the Française Des Jeux (French lottery), in which an old couple winning lottery find destinations for holiday by spinning a globe, and land on Australia. The wife say it is too far, and her husband answer with this “That’s the game, my poor Lucette”.

This used to be popular, but the usage seems to decrease as the TV spot memories grows old.

Another option:

Écoute, on a perdu, mais ainsi va la vie. On fera mieux la prochaine fois.

I view this option as slightly sadder than “c’est la vie”.

An expression from a current singer that is used by young people could be c’est rien on s’adapte :

On a perdu le match, c’est rien on s’adapte. On travaillera encore plus dur pour le prochain.

Je ne suis pas très fan du nouveau petit ami de ma fille, mais c’est rien on s’adapte.

IMHO, “I’m not terribly fond of my daughter’s new boyfriend, but it is what it is.” is a poor example. “It is what it is” is used to describe a “general situation” that directly impacts the speaker but for which the speaker has not been able to change. The daughter’s selection of boyfriend is not sufficiently general to be used with this phrase.
The most pertinent translation suggested is probably “c’est comme cà”, although English has another closer translations of “c’est comme ça”, (=that’s how it is) and that is probably what would be used rather than “it is what it is” when talking of the boyfriend; Although “Il faut vivre avec” shares much of the sense, in English the closest direct translation of this would be “We have to live with it” but again it isn’t really a good fit when talking about the personal choice of someone for a boyfriend.

In a strategic context, one may see:

C’est le jeu

perhaps less weighty than “c’est la vie”.