@Kaylo: lol, I tend to splurge on what X character does to Zelda just to avoid the "you don't know how X character works" argument. But I'll try my best to fill in the gaps!
@Riot: We talking singles or doubles? I think you mentioned beating him in teams, but MW isn't exactly known for their doubles skill. The "Buuman trap" is a nice little trick, but it's entirely based on opponent reaction. Consequentially, if he charges it, you can just let him charge then get up/get up attack when he releases. D3's dsmash doesn't have more range than Zelda's get up attack so he needs to space himself perfectly if he's gambling on the charge to save him from not getting hit.
Not being able to CG isn't Zelda specific but he loses out on an important aspect of his game. CGs are used for damage racking, positioning, and getting his moves unstale (bair says hi). D3s usually chaingrab characters to ridiculously high percentages to get over that predictable kill moves hurdle.
I feel that losing out on the chain grab balances the substantial weight difference.
Of course his grab game is good, I think he can powershield every single one of our moves and shield grab (which again can be said about a lot of characters), except for fsmash. Fsmash is pretty safe against D3, he CAN punish it if he spotdodges it and if he's near Zelda. But if he shields it, the only reliable punish against it is ftilt which is more of an annoyance rather than something game breaking. Realistically he's not going to powershield and grab her ALL the time, but whiffed/shielded usmash, ftilt, and utilt will get punished the most.
His approach options aren't too stellar since he's primarily a defensive character like Zelda. We all know Zelda's approach options are all fail but luckily she won't have to too often during this particular MU. Just don't get too Din's Fire happy if he gets too close.
If he approaches on the ground which doesn't happen often, he'll probably run up and shield or do a dash grab. If you think he's doing a dash grab, you can actually pivot grab him or just walk away and grab or whatever punish you prefer because his dash grab tumbling animation goes so far. If D3 gets dangerously close to you with his shield, again you can grab him or try to push him back with fsmash/poke with dtilt. Dthrow is really good for making D3 use up his jumps and I mention fsmash/dilt since they have an ok amount of lingering hit frames which give more chances to hit a D3 out of a spotdodge. Usmash is really good for hitting D3 out of his spotdodges, but it's better to activate it during the spotdodge since it's more punishable on shield.
If he approaches in the air, he can turn around at will by using one of his jumps at the expense of losing maneuverability. I usually try to run around him and bait one of his aerials then shield and punish accordingly. His aerials are more dangerous to use the closer he is to the ground so baiting a low aerial is good. If he's too high and used a lot of his jumps you can gamble and try to position so you're facing him and hit him with a nair/fair/bair. You could do it while he's facing away from you too but there's obviously more risk involved. I really don't recommend staying stationary if he approaches aerially since it gives more chances to space himself and use aerials. Good D3s will also mix in airdodges to try and get a ground grab in so look out for that.
If Zelda approaches ever, he can just grab her. Crossover nair to dtilt MIGHT WORK rarely, but I wouldn't bet on it.
He wins pretty much hands down if they're both in the air. Like I said before, it's best to mix up your descent. He beats our air game, but trying to hit him with a fair/bair/nair can catch D3s off guard. It doesn't solve all of her problems, but it'll make D3s rethink their options.
They both win if their opponent is off stage. D3 falls so fast and moves so slowly in the air that airdodging isn't always the best option for him if he's chased off stage since he'll be forced to recover even lower. Zelda's dair is surprisingly effective to force D3s to recover low. The best situation for Zelda is if she knocks D3 off with a dsmash or another attack that doesn't send very high (lol Nayru's?). Trying to countercamp Zelda offstage with waddle dees if D3 is above her isn't a good idea either since there's enough lag to get hit with Din's if it misses her. D3 also doesn't have any good ledge options against Zelda, with his best probably being a jump to dair.
D3 can just regrab Zelda so she is thrown offstage over and over again, it's really as simple as that. Her ledge options aren't that great against him either with her best being jumping and running away or something lol.
I dunno if I covered everything (probably not), but that's the most I could think of for the time being. I do mention punishing a lot for Zelda's advantages just because she is a good punisher and there are a lot of situations where D3 is open for punishing. I really don't mention specific moves for punishing since she can use a ton of different ones but bair and fair are optimal for kills/dilt for racking damage etc etc.
Oh yeah, dtilt>utilt/usmash/whatever is really good against D3 for kills since he's too heavy to get popped up too far/big/fat/ugly/barely any aerial speed at all/no fast aerials to hit Zelda out of the way with in time.
edit: wow that is one unattractive wall of text. lolololol, there's no tl;dr sorry