I’ve played them all at their respective times and I’ve got to go with Halo 3. Halo 2 had a better story and probably a better MP (though I didn’t have XBOX Live back then :() but 3 just impressed me on every layer it had. The introduction of Forge and Theater made the game much more fresh, fun and enjoyable and the story was just the epic climax I wanted it to be. The graphics were at their best (in terms of the artistic vision, obviously Halo 4 looks better)- bright and beautiful. The gameplay was the best overall IMO (though it does have strengths and weaknesses as you’ve said, overall it is the best): Dual Wielding, a non-scripted Scarab, Vehicles at their best, amazing BTB (and I bearly play BTB on Reach and 4), the maps (Guardian, Sandtrap, Valhalla, the Snowbound remake and of course Sanbox in all its Forgeable glory), the last truly even-from-the-start Halo game before COD influence managed to get to every -Yoink!- developer (don’t get me wrong, I love Halo 4, but I would prefer it if 343i would have taken a different route), the terminals and COLLECTIBLE skulls, the Ark mission, in fact, all the missions! I love that game so much. I don’t think I have one complaint about it and I don’t think I ever had.
Reach was the worst. It lacked the magic that Halo used to have and that 343i have (mostly) managed to retain- the Forerunners, the Halos, the Flood. The heart of the story was missing in Reach and paired with depressingly dull graphics a multiplayer that wasn’t too sure of itself laying between Halo and mainstream (COD) with the whole Loadout fiasco- at least 343i went the whole way there. Trying to get the best of both worlds only made Halo Reach a clunky and unsatisfying experience in the long run. Also, Forge World got old very fast with the rough graphics and the green blue and gray theme but Bungie didn’t address that issue, and Firefight paled in comparison with its ODST counterpart, feeling more like an Arcade shoot-sh*t game mode than actual survival.
Halo 1 and 2 were both fantastic and new, introducing the console world to a refined version of many classic FPS features and making some new ones along the way. You didn’t mention ODST and Wars which were both fantastic for what they were, and I guess Anniversary was all it tried to be (which is very good).
Halo 4 had too short a campaign though what was there was done well. The multiplayer is fun, but it seems more things are falling in place months after release rather than at release (which is a shame but is better than nothing). The Forge is great though there are technical issues (like having to buffer every time we switch to human- extremely annoying and time consuming- and the fact that there is no percision editing) that hinder the experience a bit. One thing that is actually bad in Halo 4 is Theater- we can’t do anything with it anymore and that’s very sad. Spartan Ops was great, but like Multiplayer, it had many problems at its beginning, the second half was better and hopefully season 2 will be leaps and bounds ahead of both. It seems like Halo 4 was 343i learning curve and I think Halo 5 will be much better.
All in all, I think 343 should look at Halo 3 in terms of the major three: Story, Gameplay and Graphics- they probably won’t go back on the Loadout system (which is fine) but in terms of moment to moment gameplay, anything can happen 