Torchlight 2! But there are zombies in certain parts of it (not that they're scary or anything)

If you dont mind early access titles Dungeon Defenders 2 is a lot of fun (and has a new content patch in a week ish)

Torchlight 2. Think like Diablo 2, but less gothic.

Trine 1/2

Lego games , Brothers : A Tale of Two Sons, Ibb & Obb, L.A Noire is a really nice game to play with a couple, Guacamelee, Spelunky Battleblock: Theater, Monaco

Awesomenauts maybe?

How do you Do It?

Borderlands 2 is great, I think you should at least see if she likes it. Also Sniper Elite 2, Serious Sam franchise, Saints Row III and IV.

How about D:OS or one of Saints Rows?
EDIT: just noticed she doesn't like isometrics, so D:OS is probably out.

If you both like board games 100% Orange Juice and Talisman might be good choices. Ibb & obb is also fun(and frustrating at points :P)
Then there's Don't Starve Together or maybe even Payday 2? I'm not much into FPS either but somehow some heists are really entertaining.
Unfortunately none of these give emphasis on a story. In fact a couple don't even have one to begin with :P

I know you asked for PC, but if you have a PS3 you could try Beyond: Two Souls.

As for PC, If she likes Zelda try Lara Croft and the Guardian of Light.

The Saints Row games have the best co-op I've seen in a quite a while. Completely customize-able characters and you can do absolutely every aspect of the game co-op, which is rare. Dungeon Siege III has pretty good co-op, although its top-down. Sacred 2 and Titan Quest are both great dungeon crawlers. They're both top-down by default, but you can adjust the camera to more of a pleasing angle. Dead Rising 2 has co-op, I believe. Dead Island was a lot more fun co-op than single player, even though she doesn't like zombies.

There's always the LEGO games, if she'd be interested in that type of game. Very light on the story, but they can be pretty amusing, especially if you get one with a license that she enjoys (LOTR, Indiana Jones, etc).

Brothers - A Tale of Two Sons (have her control the younger brother, and maybe play through the intro cutscene on your own - it's a bit sinister)

Orcs Must Die 2, Metal Slug, Lara Croft and the Guardian of Light, Rayman Origins/Legends?
I would recommend Resident Evil 5 too, but... zombies.

Secret of Mana

Orcs Must Die 2 was super fun - I played it with my husband. Not a whole lot of story, but still really fun. It also might get her more accustomed to shooter-ish type games (it's a FPS Tower Defense game).

Don't Starve Together - Again, not really much story, but it's hella addicting. My husband bugged me and bugged me to play it with him, annnnnd then I starved IRL that weekend we got it...

Lego games are also great for co-op, at least they have a little story and a good sense of humour!

There are so many other games you could probably get her hooked on. I would try to find games with FPS components so you can work her over towards more shooters (like Orcs Must Die 2). My husband got me started with Portal, then TF2 (medic bitch), Gears of War (ew, console) and now I play more shooters than he does... I know I love a good story too, but there are a lot of good shooter ones out there as well, and sometimes it's a nice break to just shoot the shit out of things.

I haven't played a lot of local co-op games but here is an exhaustive list of games that aren't primarily shooters, zombie games, or contain lots of crude humour. These are all the games I've played that I've also enjoyed with more than 5 hours played via Steam time. if you look at the online co-op list, these are mostly sorted in order of my playtime in descending order (most to least), so if you want something that will really last you the top of that list may be worth investigating moreso than the bottom. it's probably a good idea to check the "Local Co-op" tag on the store to see what else is out there, not a lot of people can play local co-op easily so don't expect a lot of decent/good local co-op titles to be listed here. and yeah, really hard to suggest first person co-op games that aren't shooters :p

Local Co-op:

Jamestown (shoot 'em up)
Trine (just judging off Trine 2 being real good, haven't played local co-op)

Online Co-op:

-+ for 1st person
++ for 3rd person (not top down)
unmarked are top down, sidescrollers (or other)

Sol Survivor (traditional tower defense)
Terraria (2d sandbox / exploration)
++ Orcs Must Die! 2 (third person 'shooter' tower defense, it is a shooter technically but doesn't feel like one)
Civilization V
Tabletop Simulator
Magic Duels of the Planeswalker (card game, has co-op (2headed giant version), avoid 2015 edition)
++ Dungeon Defenders / Dungeon Defenders 2 (like Orcs Must Die 2, has shooter elements on certain characters, but doesn't feel like a hooter)
Beat Hazard (probably avoid, simply because the co-op doesn't have a lot of depth, but it is a good co-op game)
-+ Sanctum 1/2 (third person shooter tower defense, might be too shooter-y)
100% Orange Juice (not co-op but still fun to play with friends)
++ Spiral Knights (f2p rpg game, last I checked I have 62 hours and haven't spent a dime)
++ Zero Gear (zero gear has some great aspects, but nowhere near as polished as Sonic)
++ Torchlight II (if you want an aRPG, a good one to try)
++ Titan Quest (same as above, but if you prefer an ancient mythological setting, get Gold edition if you do get this)
Trine 2
++ Darkspore (only playable on Origin but if you own it on Steam you can get an Origin key via support, a neat little aRPG, not much story)
Critter Crunch (co-op and MP probably won't last you too long so maybe worth skipping, but if you want something puzzlely it's worth a check)
Shoot Many Robots (a little bit of crude humour, but not like Castle Crashers, it is a shooter, but a side scrolling one if that matters)
Monaco (technically a shooter but doesn't feel like one at all)
Wanderlust: Rebirth (an action adventure with some RPG elements, gameboy-esque graphics with better graphics than RPG maker games)
Risk of Rain (technically a shooter, sidescroller survival game)
++ Dungeon Siege 3 (saving was weird with 2 players, only one player gets a save locally, not my most recommended co-op RPG but not orrible either)
Hammerwatch (very fun co-op dungeon crawler, very little story)
++ The Incredible Adventures of Van Helsing (like Torchlight and Titan Quest, just with a steampunk fantasy setting)
++ Din's Curse (grapihcs seem dated but it is pretty fun, still might want to pass, have had connection problems with the game specifically in he past)
Worms ... (versus, not co-op but might be a fun versus game to play with each other, I'd recommend Worms Revolution of the ones I've played)
++ Lord of the Rings: War in the North (not a bad game, decent side story to Lord of the Rings trilogy, not great either though)
++ Dungeonland (haven't played since F2P but it was a nice game to play co-op, might not hold you for very long though)
Hero Academy (versus, not co-op, but a nice send by mail game that's enjoyable with friends)
Ticket to Ride (versus, if you don't own it the physical game, of course)
BattleBlock Theatre (same devs as Castle Crashers but the humour doesn't seem as crude as that)
++ Lara Croft and the Guardian of Light (if either of you like Tomb Raider and want to play it co-op, top down adventure game (with shooter elements))
Rock of Ages (versus, not co-op, won't have very lasting multiplayer but a nice game nonetheless)
Magicite (similar to Risk of Rain above, without shooting)
HOARD (no campaign, nice simple style, top down and versus only IIRC)
++ Star Trek The Video Game (not the best, as the reviews indicate, but worth playing I think if you are a big sci-fi fan)
ibb & obb (puzzle)

If you are open to non-steam game, Blizzard games are always solid, I can personally recommend StarCraft 2 if you both like RTS, and World of Warcraft is fun even if you just level up to to whatever the max level is these days and do some dungeons upon hitting the max level.

edited: SteamGifts formatting is as unintuitive as formatting comes

ibb & obb (it seems simple, but requires a lot of coordination and communication between the two players).
Child of Light (maybe the player controlling the elemental can get bored, but it's an amazing game with amazing visuals, story and soundrack (that soundtrack!))

Lara Croft and the Temple of Osiris
Hammerwatch (top-down; some friends that only played FPS before got hooked with this one)

Trine - it's beautiful, it's fun and having coop partner helps to get to all the hidden places (I'm not sure you even able to get everywhere if playing alone). I actually think that here coop better then playing alone, since you don't need constantly switching between characters to solve puzzles.
Never Alone - haven't played it myself yet, but probably will get one on the sale. Heard a lot of good things, looks wonderful and come on, you can play as an arctic fox! ^_^
Monaco - if she like planing and stealth strategy and don't get frustrated when those plans got screwed and turn into running and hiding chaos - then it's surely fun!

Dying Light maybe? Zombies or "infected" yeah but also a good amount of human enemies. I dunno.
Van Helsing?

She likes FPS or not? You said at first that she doesn't but in the edit that she does.
What about 'payday 2'?

7 Days to Die. Kill zombies. Build penis base. Always fun.

Lara Croft and Guardian of Light.. duh :D

Try BattleBlock Theatre - My girlfriend doesn't like Castle Crashers either but she enjoyed BB
Also try: Sanctum (1 and 2), Shank 2, Guacemelee!, How to Survive and.. Mortal Kombat 9 - so refreshing.