I love the basic, and very heartfelt, notion, but do not like any of these specific ideas.
Overall: By and large, what this means is old and high alliances get a MASSIVE dump of loot/gems, widening the gap between the haves and the have-nots. Sure, you could only start tracking on new achievements, but then the battle space is suddenly going to become ultra-ultra competitive for a while, and who wins that? The long-time players, while the mid-to-early players become punching bags so that the milestones can be earned. On top of that, this sounds extremely exploitable without some very careful thought about maintaining player history. Swapping alliances, starting new alliances, alt and zombie account manipulation would all be rampant if it were not done just so. The fact that Alliance-hopping could help you achieve these goals is only a small side-irony here.
TIME: The best of these, although not the War streak. Here there be Dragons! But directly rewarding time in an alliance seems pretty good.
CHALLENGE, RAID STREAKS, TOURNAMENT: Good basic concepts, but not really milestones per se. Recommend moving these to a separate category concerning “Alliance Loot” or some such. I’d vote for that.
STRONGHOLD, RAID TIER, STORY: All have individual Missions already, and adding them as Alliance missions doesn’t have much value for instilling loyalty, see above.
MISSIONS: Missioning missions? Meh. Not compelling. If a one-time thing, why not just increase the Mission loot? If ongoing, not a Milestone, and presents many problems for those on vacation, etc. Also, coordinating everyone’s Titan Mission seems… difficult and perhaps not worthwhile.
HERO: No. Please, no. If you have high-level Heroes and Troops, these are their own rewards. SGG has actually created a place that has whales but is not overly sensitive to them. Please do not feed the whales.
Great idea, no vote.