I actually felt that Mass Effect 3 was the best in the series. A disclaimer: I played through for the first time after the Extended Cut DLC came out and with it installed, so I never experienced the initial frustration with the ending as many did. This is not to say that ME3 doesn't have its flaws, but I think it has fewer than the other two games in the series.
(1) Plot: While Mass Effect 3 isn't the first game to use an "apocalypse" scenario for its story by any means, it does a fantastic job of (a) giving the player a sense of urgency and (

laying out the political, difficult, and emotionally challenging decisions that would need to be made in a war for one's survival. I have a hard time discounting the different plotlines (i.e. genophage, quarian/geth, etc.) on the ground that the are "expected," as the OP does here. Any work of art has themes, and when you have a series one is supposed to build upon those themes to create some kind of ultimate outcome. For this reason, I had the hardest time getting used to Mass Effect 2 (which many people think is the best into the series), because I thought the Collector/Cerberus plotline was really random/didn't initially build off these themes. I wound up enjoying Mass Effect 2 (it was definitely better than Mass Effect 1), but it took awhile for me to get into it. Although I was not 100% satisfied with Mass Effect 3's ending (even with the EC installed), I enjoyed how Bioware decided to conclude the majority of themes/scenarios over the course of the game.
(2) Characters: While there were fewer characters in Mass Effect 3, and while I missed some of my squadmates from Mass Effect 2, I have no problems with the general decision to include fewer characters on the Normandy. First, as this is a total war for survival, the world can't afford to have every soldier/fighter with any degree of special talent on the Normandy. It wouldn't make sense. The war is going on across the Galaxy, and the Galaxy's champions, therefore, also need to be spread across the Galaxy/have their own ideas of the best way to help. For this reason, I thought cameos/limited interactions on the Citadel were a great way to meet old friends while addressing this concern. Second, the Commander's squad was somewhat oversaturated in Mass Effect 2. Each squad member should have a somewhat unique role to play. There were certain characters in Mass Effect 2 that, other than for a loyalty mission and maybe one other mission, I never used at all. Finally, having fewer characters allows for more character development, not only with the Commander but with each other. I particularly enjoyed seeing various characters interact with each other/move around on the Normandy, from having Javik debate with EDI, to having Ashley passed out on the floor after drinking with James. Not all development has to go through the Commander himself.
(3) Exploration: Planetary exploration in between missions was extremely tedious (and often quite boring) in Mass Effect 1 and Mass Effect 2 (although it was great to see all the hard work from that pay off in Mass Effect 3). Mass Effect 3's search and rescue makes it less tedious without making it too uninteresting or useless. True, I wish Bioware had come up with some way to fight the reapers after becoming detected, or introduced upgrades that make it easier to evade them, but that wasn't too big of a deal for me.
(4) Combat: Except for the minor frustration I had with the "spacebar does everything" mechanic, I thought combat in ME3 was the best in the series. The enemies were varied and used a variety of tactics (this was best executed with Cerberus), and one could be creative with the variety of powers squad members had to offer. I have only two major criticisms. First, a lot of weapons within the same class (i.e. shotgun, assault rifle, etc.) were too similar to each other. The upgrades, with the exception of the sniper rifle upgrades, are not unique/interesting enough to make weapon customization/use all that interesting. The different DLC packs have fixed this somewhat, but I wish Bioware had done more with it. Second, Bioware removed heavy weapons as actual, permanent weapons. Apart from being unrealistic in that heavy weapons are just "found" randomly, without ever actually being used by the enemies themselves (I don't recall any reaper forces wielding a blackstar weapon), it removes another possible element of strategy in some of the larger battles. Instead of making them temporary, Bioware could have made the ammo rarer/more expensive. Considering how flushed I was with credits at the end of the game, the latter would have been considerably more exciting that blowing all my excess credits on Spectre weapons that, while powerful, were less interesting.
(5) Multiplayer: I'm not going to go into much detail about this (I consider the ME3 multiplayer to be a separate "game") other than to say that it's definitely the best in the series. I'm still playing it to this day, alongside my other playthroughs of the single player game.
(6) End Satisfaction: Minus the discussion with the Catalyst, I was satisfied with how the ending played out. I had no problem with the notion that the Commander had to sacrifice himself to save the world, nor with making the illusive man an end villain. I also enjoyed the cutscenes that (I gather, the EC introduced, as that was enough for me to build closure with many of the characters under the circumstances). Although I'm sure they've been said before, I will voice my criticisms of the ending. The first, is that the inclusion of the Catalyst is random and does not serve as an effective end to all of the game's themes. Depending on how you play the game, you may have already proven the Catalyst "wrong" with respect to the organic v. synthetic conflict. If the Catalyst winds up disagreeing with you, that's fine, but it definitely warranted further discussion/debate. The second, is that the ending did not make use of Harbinger (in my opinion, an excellent villain) in any major way. There should have been SOME kind of a boss fight, even if the Commander ends up defeated/it's impossible to win. Finally, other than the cinematic showing the fleets emerging to meet the reapers in Earth's orbit, collecting war assets did not play out in any major way, apart from the interlude in between the first and second halves of the last mission. I'm not saying that all the races should have actually had to be seen fighting the reapers on the ground, but you should have at least been able to receive some update on how the Geth, quarians, batarians, volus, etc., were doing in the battle (in a manner similar to the com station where you get one last talk with the characters who aren't in your squad). I understand that the bulk of the forces were needed in orbit, but that doesn't preclude the addition of further details to keep things interesting.
It wasn't perfect (other than perhaps Baldur's Gate II, no game is), but I felt more satisfied finishing Mass Effect 3 than I did with finishing Mass Effect 1 and 2. For me, the journey was enough to override any dissatisfaction I had with the ending.