People are saying this, and I agree, "too many bad match-ups"
But what nobody's saying is which ones should change for Bowser.
I totally agree! (well, on the posting part)
I've recently picked up Bowser and I swear he has an advantage against Captain Falcon, Ganondorf, Donkey Kong and Jigglypuff. The biggest reason behind it being his Fire Breath's ability to keep the former three at bay when needed.
Captain Falcon's aerials have trouble getting past Bowser's tilts or, worse yet, Bowser's forward air (when Bowser is chasing him off the ledge). Add that to Bowser's Fire Breath and the poor Captain has a difficult time approaching Bowser. In Falcon's favor, however, is his forward-B's anti-Bowser spiking capabilites. If Bowser's an idiot he'll be spiked at each edgeguarding attempt. However, Captain Falcon's forward-B can only be done when he's close enough to the ledge - and many of Bowser's best attacks send Falcon flying at a low enough angle that he can't just throw his forward-B out - and even then Bowser's forward air beats Captain Falcon's forward-B. Bowser is a big target for knees but with a very protective forward air and better spacing abilities, Captain Falcon is hard pressed to land one.
Ganondorf isn't quite as easy - his forward-B is great against the shield-loving Bowser. Unfortunately for Ganondorf, his approaches are also quite limited. Fire Breath (relatively safely) shuts down Ganondorf's ground game (although when he's close he'll hit Bowser will a jab or a tilt and it'll hurt) and since Ganondorf's aerials are so slow, a Bowser should be able to powershield, dodge, roll, whatever to avoid damage. In Ganondorf's favor comes his powerful down air and it's almost guaranteed KOs against a low recovering Bowser. In this case, Bowser is better off recovering as high as he can - Bowser's up-B should be fast enough to stop Ganondorf's other aerials from coming out. The key is to keep burning the very slow walking Ganondorf and tilting him away when he gets too close.
Against Donkey Kong I find that they're almost even but that Bowser has a slight advantage due to, again, his Fire Breath. Whether it's Bowser hitting Donkey or Donkey hitting Bowser, either way basically puts them in a position where Bowser can use his Fire to painfully push Donkey Kong back or force him into the air. After a while the damage starts to accumulate which leads to Donkey being edgeguarded by... more Fire! Giant Super Amour Punch is very scary to Bowser though and making one small mistake will always lead to getting Bowser's brains punched in. As well, Donkey Kong's down-B comes out slightly faster than the Fire (or at least it appears to) and can knock Bowser in exchange for only about 1% of Fire damage.
Against Jigglypuff, who can combo Bowser into oblivion, it becomes a matter of not letting her get close enough to initiate the 'wall of pain'. The key there is forward air (NOT fire since Jigglypuff happily flies over it and hits you). She's also susceptible to the strong back air (always done way above the ground - it's good for stopping Jigglypuff from getting back on to the stage). An upward angled forward tilt and an up tilt are also great anti-Jigglypuff techniques. Overall I find that Jigglypuff has a much harder time getting in to Bowser than he has keeping her away.
... Of course, I'm still quite new with Bowser and it could be that I'm winning my battles on novelty alone (probably not since projectile characters absolutely destroy him - Wolf's blaster should be banned in tournaments against Bowser!). I don't feel that I'm good enough yet to have my Bowser opinions count towards the chart so I'll see what people think about those four possible advantages. The Jigglypuff one especially seems a bit iffy since Bowser suffers from the 'wall of pain' more than anybody else that I've seen, and her ability to weave in and out make it a bit mindgame battle.
By the way, my apologies again but it won't be until this Saturday when I can get back to working on the chart. My goal is to be able to fill up the entire chart in that day (hopefully to most people's satisfaction). Can you post a link concerning the Japanese tier list stuff? That'd probably help out.