It's harbor silted up at the end of the first millennium, and Judea has been one of the most fought over spots on Earth since the Bronze Age (there's a reason no great empire ever rose in Judea). It's also too close to the Arabs who will be settling in sizable numbers in the area in Late Antiquity with or without Islam. It's somewhat remote from rich provinces like Egypt or Syria or Africa.
Even more than that, IIRC there has never been a state based in the Palestine which was not pushed back or destroyed by invaders from Egypt/Arabia/Mesopotamia until the present day Israel, which can only work because of massive degrees of foreign support, a major influx of immigrants (in the beginning), an excellent military system, and no small shortage of luck...in short a perfect storm.
Judea is the adjacent province to both Syria and Egypt. Arabs rose mostly after the third century with the first ones rising at Palmyra. Others were mostly tribal like the Nabateans. In one timeline,Greeks and Romans would leave the Petra and surroundings alone and build massive settlements in Golan Heights,West Jordan,regions around the Galilee and Caeseria Maritima. You could have large amount of settlers from the core regions of the Roman Empire like Italy,Gaul,Hispania,Greece,Anatolia into this new capital in an effort to make it the center of the new empire. Arabs who come and settle inside can be assimilated quite easily. With a strong provincial government and strong borders around this region,Islam as in OTL couldn't exist. It would be a lot different.
Hmmm...Islam would definitely be different from OTL, but there's too much to happen with the Sassanids for some movement of desert nomads to not become a possibility. I'd say that a capital at Aelia Capitolina/Jerusalem, with a post-Constantine POD, is only possible with a total Christianization of Arabia, and even then is risky.
A bit ambitious, but maybe Tolose or Bordeaux would be good.
Centrally located near Italy, Gaul and Spain, with the possibility of an early Canal de Midi connecting the Atlantic and Mediterranean (even horse-drawn); Which would improve communication with the Channel Fleet and the Rhine.
And while not as good as the Alps, I think having the Pyrenees south and the Massif highlands north is an alright position.
On the same vein, would Faventia (modern Barcelona) be a possibility? Still close to Gaul, but defended behind the Pyrenees and also close to Spain's mineral wealth?
How big was Marseille at the time?
IIRC Massalia was essentially outgrown by other cities in the area during the Roman period. It remained an important city for education in the West and generally had a good bit of prestige, and so would be a possibility particularly if a premium is placed on naval access.