What don't you like about Bowser? I haven't played Kirk's in a while, but I always felt like it was a very doable MU. She has a lot of ways to keep him in the air, where he can't just safely up B out of everything forever.
Sorry for the delayed response. Bowser has tons of tools to use against Zelda when it comes to fighting on the ground and that's what makes the mu very difficult. Its very heavily based on kicks and keeping Bowser in the air, you are absolutely correct in that aspect. The hard part is that Bowser can kill Zelda at extremely low %s (57%) off the top of sv from a grab>uair, upb can pretty much do whatever he wants it to, and his crouch is extremely hard for Zelda to do anything about when he can easily dtilt out of it to push her back. Dins is useless on the ground as well bc he can clank them with upb/dtilt or ftilt which has an amazingly good range to keep him safe from punishment if he's clanking them and you're trying to use them as a distraction. 90% of the time if Bowser is at a low % and you're casting dins, he will dash attack (which was also buffed with 2 hitboxes) right through your dinky fireball or even during the startup and land a solid hit right on you. THAT is extremely detrimental bc it can also kill you.
Bowser also has enough armor on side b that he can completely armor through a critical kick on start-up and grab you and do whatever he wants. Basically Zelda needs to stand back for the most part, and being that hes so good on the ground with an incredible vertical range, she suffers big time. The most Zelda can hope for is to land counter kicks, bait his approaches, avoid using dins (one of her greatest strengths), and pray that she doesn't get grabbed. Grabs will generally lead to death in most cases from Bowser even with decent DI. Especially now that his grab range has been greatly increased.
Something else to keep in mind, Bowsers ledge attack is arguably one of the best in the game with its range and kb, so it makes edgeguarding him also extremely difficult because if he gets the ledge he pushes you back anyway. You can be daring and go for the dair but his upb may end up hitting you. If he lands on stage, he can hit you with the recovering upb>upb again on stage and depending on your % you will die. Playing good Bowsers requires excellent juggling capabilities and a good keep away game which makes it one of her hardest matchups considering he doesn't have to do much to get through her multihit smashes.
Tips for the MU:
+Don't be afraid to get hit by Bowser's new quake hitbox if you're in range. If he hits you with it, you typically come out of hitstun before Bowser can get back on his feet again and are able to land a nice critical kick.
+Grabs are your friends and keep in mind that if Bowser is behind you and you are shielding, he may attack your shield and allow you to grab him while his hitbox is extended in front of you. Just be careful doing that because it can become predictable.
+Use farores wind and mobility very wisely as he can upb you anytime you cancel out and possibly kill you. Use it more for tech chases than movement.
+Try to build damage quickly in the beginning so he loses some of his armor once he reaches 100%. It makes killing him a bit more manageable.
+Stand near the ledge when Bowser is on it, shield the getup attack (below 100%) and when he retreats back towards the ledge, grab him for a swift bthrow to get him back into the air or kill him w a din trap.
+IF you land a LC nayru>jab>ftilt>jab>fair that will be a great opener. And if the bowser has bad di, LCnayru>jab>ftilt>jab>ftilt>uair(electric+sweet) will do great damage. However, BIG ''ifs'' there.
EDIT: Thinking back on this, the real issue is killing him. Bowser will kill you with: uair, fair, upb, sideb(grab or slash), usmash, fsmash, or down b. Zelda can kill Bowser with Fair/bair crit spot at decent %s, utilt (high%s), MAYBE a good back hitbox of dsmash, uair, and bthrow at high%s. All of those kill moves of Zelda's are much harder to land than Bowser's kill moves so it comes down to kill power and the situations you have to take advantage of listed above. ((Sorry for the book, just trying to be helpful.))
Hope this explains/helps anyone that may be having trouble with Boozer.
(You could always use Wavebuster's approach and use downB....)