If you complete either the community center or the joja upgrades, you can progress to build the theater and fix the boat to the island. There are some important differences that may affect gameplay, though.
Each community center bundle has a small reward that can help complete remaining bundles, like dish o the sea which has a fishing buff.
There is no joja upgrade that correlates with the bulletin board, which grants two hearts with most villagers.
If you finish the community center, Pierre's will be open on Wednesdays, but Clint will close on Fridays.
If you finish all the joja upgrades, you will get a joja cola machine. The theater will be located at the site of the warehouse (instead of at the jojamart) and there will be no community center at all.
I found the major drawback to the joja route was the values of bundle items. A sampling of seasonal foragables or local fish, for example, costs far less than the correlating joja upgrade.
Joja can be a fun way to specialize a playthrough. So if you don't want to fish or mine, and only want to plant flowers. Or if you only want wool and cloth and to do all the tatailoring.