I think that generally the problem is that the third one is where the series falls apart because they don't have any exciting story left. Usually, we see:
-Game/Movie 1, where the universe and characters are introduced. Generally has a bit of sloppiness, but that's forgiven because it's a new property and you can see exciting potential, and its also lean enough that the experience isn't ruined. Example: Assassin's Creed 1, where you have only a few weapons and techniques, but everything is fast-paced.
-Game/Movie 2, where everything is bigger, better, faster. The people making it know what they are doing, they have the chance to take the skeleton of the first game/movie and add all the little bits that seem good, and they have the funding to do so, which leads to what is usually the best X in the series. Usually people also take this time to do the "Hero refusing the call" archetype, which leads to problems later on. Example: The Dark Knight, where you see great character development, a good sense of Batman using darkness/brutality and high-tech gadgets, and some phenomenal acting because they don't have to do any establishing work anymore. Also, Assassin's Creed 2 (by which I mean the Ezio games in general) where you have some variety in tools and they introduced new concepts like the Assassin recruits.
-Game/Movie 3, where everything falls apart. Thematically, because most trilogies use the second part to have the hero abandon then recommit themselves to the goal, there's nothing to do but either faff about or retread the same ground (See: Dark Knight Rises, where there is not one but two separate "rebecoming Batman" moments). In case of games, it's even worse. People expect to see new things added, but the developers already put most of their good ideas into the second game, which means there is nothing to do but add bloat. This leads to stuff like Assassin Creed 3's Homestead nonsense, where you have to micromanage an economy, keep showing up to do unfun little side quests and minigames in the hopes of unlocking some helpful tool, and occasionally dropping everything to go protect a trade caravan, rather than play Assassin's Creed (i.e. assassinate people).
Basically, the 3rd installment is usually the most hated because it faces the expectations created by the second X, but has little to nothing to contribute other than tying up loose ends.