It is true that 2014 was relatively poor for the 3DS as well, but i don't recall any of its games included in previous top lists either...
From the games you played, Smash Bros is already kind of included, Bravely Default is Overrated (too much repetition and not enough genuine challenge) :) , but Fantasy Life is definitely better than at least a couple of your entries...
I am surprized you didn't like it more. It is actually a family-friendly handheld Skyrim. A nice charming main story that is easy to complete and acts more as a tutorial, plenty of things to do, many different classes to master, and a wonderful crafting system. Plus really great production values for a handheld game and an incredible localization.
Maybe you didn't like its presentation style, or you thought it is just another run-of-the-mill jrpg. But it is not. I have been playing "hardore" crpgs for decades, and i was plesantly surprized by this title. When i look at its metacritic score, i think this is one of the most underrated games of recent years. Maybe not the best rpg ever made, but in a dissapointing year like 2014, how many games were better than it?
80 days? 80 days is just an interactive novel.
The Crew has many problems.
Diablo III is a boring click-a-thon. Just because it is addicting, doesn't mean it is a good game, or fun. Drugs are addicting as well... Plus, it is not a 2014 game...
Endless Legend is just a boring micromanagement chore. It has many gameplay elements that don't mean a thing. There are few actual decisions you get to make that matter. Plus its AI is worse than Civ. You criticize Civ poorly for poor AI and meaningless choices (i agree), but then when a Civ-clone with more of the same problems comes around, is in Top 10 of the year? Just because it has different races? Yeah i get it, instead of mastering one single micromanagement formula to win deity every single time, you get to pick which slightly different micromanagement formula you will use before the map is generated...
Another game that is seriously lacking is Xenonauts. I really like older Xcom games, but this one is just a bad imitation. It just tries to capitalize on the nostalgia of gamers. It is not that good. Too much tedious after a while.
Infested planet i haven't played.
Age of wonders has good AI? Seriously? Since when? All it does is cheating. Spamming wave after wave of units and rushing. Actually, both this and Heroes of Might and Magic 6 have the same problem: No strategy, just rush before you get rushed. Really boring and tedious game, the building element serves no purpose, might as well make it tactical and acquire units with "points".
Beyond Earth is actually far better than both strategy games you included on the list. Of course, it has no good AI as well, but it has different strategies to pursue and many choices to make, Plus far better production values. I don't believe it belongs to top 10 games of the year, but in a list that includes those other two? Come on...
A strategy game is about thinking and well... strategizing. If all you do in a game is following/micromanaging a winning formula that is the same every time, where is the strategy?
Now, for a game that i believe you overlooked:
Alien Isolation. The most revolutionary survival horror up until now. Instead of being just an action/adventure game with some horror surprizes and/or over the top gore, it actually is scary all the time. In proper difficulties, you are even scared to walk. Plus pretty faithfull to a movie classic. It has some flaws, but it definitely belongs in Top 10 of the year...