Big, big changes. First of all, I do not think JA would be VP. A Southerner (and almost certainly a Virginian) would be necessary for sectional balance. Thomas Jefferson comes to mind but Patrick Henry was actually much better know at the time, although he had been an anti-Federalist.
Franlkin was certainly a Federalist and a nationalist but I am not sure he would have been as supportive as GW was in supporting a Hamilton like program of assumption, tariffs, internal taxes and a national bank.
Would there even have been a Hamilton program? AH was not GW's first choice for the Treasury but if Franklin had offered the post to his fellow Pennsylvanian, Robert Morris (as GW) did, would Morris have turned Franklin down and recommended the young AH?
Without a Hamilton program, including a tax on whisky, would there have been a Whisky Rebellion? If there had been, I think Franklin would have been much less likely to threaten force against his fellow Pennsylvanians and much more likely to try to talk things out. Would this have just emboldened the anti-tax rebels?
On the other hand, Franklin was much more anti-slavery than GW. As a practical matter, there was not very much a President Franklin could do about slavery but he could indulge in a symbolic acts which might support the manumission movement in the North and piss off the Southern planters.
I don't think Franklin's foreign policy would have been much different from GW's. Neutrality was an obvious policy for a weak new nation.
Finally, a President Franklin could devote a significant amount of his time to supporting educational and scientific developments in the new country. Perhaps GW's proposal of a national university could have been realized by a President Franklin.
Your obedient servant
AH