Makes two of us who're wondering that. But I guess it depends on the whole focus of the Austrian empire at the time of the marriages. If the empire is focused on strengthening their hold on Italy, then the Savoyard match is the way to go - assuming that Maria Anna's sisters marry where they did OTL. If they're interested in Germany, Sophie's sisters' marriages of OTL are the way to go. Of course, it might not be as black and white as simply one of the other. There could be other ladies/matches considered.
For instance, a POD in 1807 might mean that even if Maria Luise is married to Napoléon, the duke of Modena still marries one of Franz's daughters as opposed to his niece. OTL what happened was that Francesco IV of Modena was betrothed to Maria Luise, but then life happened: Austria made peace with Napoléon, Franz II's wife died, Alexander rejected Nap's suit for the hand of a Russian grand duchess, Franz married the duke of Modena's sister, and Austria offered Luise to him. Now, if Luise were married off to Francesco (she'd be 16yo in 1807, so marriageable age), it would mean that if Austria were to offer an archduchess, the first lady available would be Maria Leopoldine (b.1797). She's a bit young for an 1810 wedding, only just having turned thirteen in January 1810... But the Habsburgs have married uncles to nieces (Modena being a case in point), so they might not see anything wrong with a thirteen year old bride. Alternatively, they might wed Luise to Nap and consign Leopoldine to marry Modena. She'd be 15 in 1812 (when Modena married OTL).
Still, considering Leopoldine's antics OTL in Brasil, it would make her a much stronger force to be reckoned with in Paris (in time) than what Luise ever was.