I ended up doing most of it before I finished the game. Collected all the Peg Leg Trinkets fairly early and later all the Almanac Pages as I went along, did all the Naval and Homestead missions, liberated all regions of both cities and all the forts in the world, and leveled up all of my recruits all the way except for one. Most of the stuff I still need to do is over in the Frontier; I still need to collect all the feathers and chests (I cleared the cities of chests already), as well as do a few of the club missions and unlock more of the fast travel locations in the Underground.
There is a lot to do in this game, no doubt. However, I can't say that all of it is consistently good or completely worthwhile to the rest of the game aside from being more stuff to do. I really enjoyed the Homestead, Naval and Peg Leg Trinket missions, but a lot of the more minor side missions fell a bit flat for me.
The assassination and delivery missions are kind of soulless; for the mail courier missions, you go up to a guy and without much explanation at all, a handful of other icons appear on the screen, to which you go and whoever is at that location gives you the same exact line of "You have my everlasting gratitude, sir." There's only ONE line for that exchange! Considering each of those mail courier missions has you going to five or so people, it quickly sticks out as something that could be done better.
The crafting and trading systems are a bit overly convoluted and not done very well from a menu/UI perspective, especially considering just how much of the side missions and collectibles are tied into that system (chests, Naval and Homestead missions), and they don't reap as many benefits as, say, the economy system of the Ezio games, where you're constantly getting more money to spend on buying more shops to get more money (as well as upgrading your armor and weapons). Whereas in Assassin's Creed III, the crafting system requires you to basically stop the action and sit down for a significant amount of time, which makes it more of a hassle than anything.
Overall, I still enjoyed running around and doing a bunch of the side missions and I am really impressed with how they changed the different systems and side-missions to fit the context of the new setting, but after doing most of it, I couldn't help but think that they could have done a bunch of small things to make those minor side missions more enjoyable and worthwhile, and that the side mission and economy aspects of the game were handled better overall in the Ezio games.
@cmpLtNOOb: The DNA Tracker menu in the Pause screen tracks your progress with the major side missions like the Homestead Missions (it lists each member of the community and the missions they have), but I don't think it shows when in the story progression some of those missions can unlock. I had the same problem of not knowing when some of those Homestead missions become available; it turns out that the last couple of those only show up really late in the game.
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