I think Pippin flies over many adults' heads. The pair to my right had no idea what was going on or why people were cheering so hard; they didn't get the show or what was happening beyond the physical feats. It's a bit of an odd show, one many of us are familiar with so we've come to love or respect its oddities. It's one that warrants some questioning and digestion.
It would be great if you could take them to see both shows, of course. If you must choose one, it's hard to know which they'd prefer, not knowing your daughters. I do know word-of-mouth for Pippin seems consistently good. I haven't heard many folks say they felt disappointed by it. It also did quite well with Tony noms & Outer Critics' Circle awards. And their box office has been pretty consistently trending up since opening, I think -- a sign that others feel that way.
Since both shows have recordings that are available on iTunes and YouTube (Matilda's London cast and Pippin original Broadway) I say let them listen to some of the songs of both and then see which show they would rather see. Both shows are GREAT choices.