The Skyward achievements are intended to be long term goals slowly completed over the multiple phases of the Restoration (though some players have already pushed to get them completed).

If your goal is Skyward Points, you should be working on the Phase 3 achievements while they're current since they will have the highest point values until Phase 4 is released (when they'll be reduced in point value like the Phase 2 items were). Once you have the Phase 3 achievements completed, go back to work on the Phase 2 achievements.

The Phase achievements themselves are based on number of items submitted so the points don't really matter for them.