As long we're talking of an identifiable ATL France, Paris would remain a main center : at least since the IXth century, it was considered as such in spite of not having a Carolingian palace and even during Merovingian period, the division of royal ficus genreally focused on giving each king a part of Francia proper (meaning the region between Orléans and Metz, roughly).
Marseilles, on the other hand, wasn't really part of France as it was understood then (Provence being fairly peripheral) and didn't began to be before the XVIth century at earliest.
Now, if we're talking of a capital in the rough region of IOTL France...
how could it have been more prominent?
Marseilles simply didn't "cleaned" its orbit : you had a lot of other cities in the region that lived their own and could claim regional leadership at times :Arles, Avignon, Aix mostly. In fact, these cities tended to play a more important role during Middle-Ages and part of the Modern age, Marseilles going trough cyclical crises.
There's many reasons for that, but eventually one key difference between Marseilles and Paris is that while Paris (or the whole Francilian region) is set in a region without real geographical obstacles (at the contrary, agriculturally prosperous, and rivers allowing hinterland and coastal trade alike) while Marseille's territory is really quickly ended by a set of highlands that "forces" the city to look to the sea and coastal plain.
Another issue is that the multiplication of cities in Provence comes from Roman times, with each of them being fairly small (an average of, roughly, 2 000 inhabitants) but with an important enough sense of identity. You'd need Marseilles to create its own contado out of it (necessarily neutralizing Aix) to realize something. An immediate obstacle for this being that Marseilles, compared to cities as Montpellier, didn't really had a large municipal autonomy before the XVth century, being stuck in a loop of conflcit between patricians, counts, pope, abbatial power.
That said, there's nothing impossible making Marseilles more important it is today, but I'm not sure it would be trough wanking it : maybe butterflying away one of its regular contractions (for instance, preventing Peppinid takeover of Provence; or Marseilles playing a game of balance between France and HRE in order to increase its regional importance and take on the hinterland) and slowly building up Marseilles' power trough the TL : there's nothing really implausible eventually. But there's not a single PoD that could ensure it would happen IMO.
On the other hand, if you manage to allow Marseilles taking on its immediate neighbours and maybe allowing the city to pull a Venice by expanding its hinterland territory, there's not a single reason why it couldn't happen either, at least for what matter Provence and/or the general Rhodanian axis.
I remember someone making a Massalian empire TL, so that might do the job.
Massalia had a fairly limited territorial control in Gaul, even in its territorial apogee in the Vth century, while it was maintained trough a series of outposts and semi-hellenized establishment like Rhoudanousia and Thélinè (Arles) that allowed to control the Delta region and a bit beyond, it was less a chorè than a mix between a chorè and political network (which was called "Cities of Massalia", Poleis Massalias"). Note that colonies of Massalia such as Nikaia (Nice) or Agathè (Agde) never really was under their metropolis' control but were managed on their own, a "special" relation to Massalia being largely based on symbolic features (or in the case of Emporion, not even that).
The problem of Massalia are essentially the same than Marseilles, albeit differently : the city is still stuck between sea and step hills, it is surrounded by relatively powerful neighbours (Salues mostly, but as well Cavares, Volcae,etc.) doubled down by their relative cultural isolation.
It's why a significant part of their controlled hinterland
was lost to them in the course of IVth and IIIrd centuries, Celto-Ligurian peoples (notable Salues, Cauares and Volcae) advancing slowly in spire of Massalia's best efforts, which ended to stuck the city to the immediate coastal plain. It's basically the reason why the Roman-Massaliote alliance was a thing for the Phocean city : they needed some support to, far from building up an empire, prevent being even more pressured on by their neighbours.
Arabs invade first by land then by sea, Marseilles is used as their primary base and they leave it largely alone or build it with oddities like a library and sewer system. Population increases faster and the city gains control of the Western Mediterranean trade as capital of the Cathar Republic. Ultimately it is conquered by France after Barcelona and Genoa are sacked by the Emirate of the Balearics and Granada. By 1550, Marseilles has a greater population than Venice and Madrid combined, greatly influencing French culture and language. With the deatruction of Lyon and Geneva in a series of wars over the next three centuries, only Paris and Marseilles remain as focal French cities.
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Marseilles was fairly declining by the VIIIth and IXth century : assuming Arabs manage to hold on to the territory they controlled after the 734, which included Avignon and Marseilles, it would likely take the same form than in Lower Languedoc in the same period, namely a negociated submission and local elites remaining in charges which would mean
Maurontus, as provencal patrice, would likely still rule the region under their remote suzerainty, while Arabo-Berbers would likely be unable to set up more than one garrison (likely in Avignon) due to their systematic shortage of men (IOTL, they controlled Arbûna/Narbonne directly, and that's about it).
The incoming Berber revolt would have probably similar results than IOTL, meaning isolating and rending vulnerable enough places without firm control.