Admittedly I'm a scrub who has only ever played CPUs so far, but I tended to struggle with heavyweight characters the most, notably DDD and Bowser.
Only picked up Inkling as a secondary two weeks after launch, but the key to fighting heavies now, especially Bowser, is remembering that you have to respect their air game and their armor, given that the former has been so massively buffed by fast jumping and low endlag. Don't follow them into the air until they start to fall, ideally, and reverse aerial rush Bairs for the disjoint if you must contest an aerial approach, but the key to these matchups feels like forcing a grounded fight. Grounded combos (be that air to ground, ground to air, or ground to ground) seem to be the key, as air-to-air strings just aren't terribly safe when Bowser can Fair out of anything that's not true. Also, Neutral B is a great B-reversed tool that you should treat like almost like Bowser's flame breath mixed with Fludd, in that it's far better against these slower characters. That, and leaning on splat bombs helps to punish grab or aerial approaches-- particularly the uncharged high throw. Oh, and, this will sound ridiculous, but Fsmash more. Stupid as that sounds, it's your longest-reaching grounded non-special, which is extremely important to punish and read with at every opportunity-- heavies often can't punish it as readily as a quick combo character or such, so it's a bit safer than you might think. Also, Ftilt to punish run-ins is decent. And never jab Bowser. If you can punish with
any move, Utilt or grab tend to be as near to optimal as you can get, and use Nair much more than Fair (as the latter is more of a risk against their powerful aerials).
Welp, those notes degenerated into chaos by the end. My bad.
As for Chrom (and, by extension, other swordies), Bair is similarly your only way to contest aerials directly, which works best by dashing back whenever you see an approaching hop, to get space for a RAR. That said, it's not great to contest Chrom's Nair from anything other than the upwards diagonal or directly below, so dashing under tends to work as-well-or-better, unless you can get enough space to jump only after Chrom starts to fall, as that will get a nice angle. Splat bombs work wonders to cover platforms and slow down neutral, but your basic game plan is "stay as low as possible while abusing tricky dash dancing", as Chrom's aerials have a pretty serious blind spot directly below him. Dtilt and Utilt are great, and Up B is your best tool for contesting his recovery (which you need to be very, very careful about and actually should almost always instead go for ledgetraps with splat bombs and whatnot). If he stays grounded (which I rarely see unless I tilt someone by parrying that one dude who only knows how to SH Fair), Fsmash's range is important against Ftilts and such, as trying to dash in or short hop rather than Fsmash is a
big mistake when he's likely to either repeat the tilt or react to movement with jab string or whatnot. Careful with that, though, as Chrom's speed makes the commitment pretty relevant... If I'd played more Inkling, I might have gimping setups in mind, but as-is, I just ledgetrap and respect aether, rather than get counter-gimped by the spike.
Personally, I don't feel like Inkling has many terribly weak matchups. Swordies are tricky, but, like Smash 4's Mario, that doesn't necessarily make them terrible matchups if you can respect their sword reach and such. Though, I will agree that Megaman feels incredibly difficult, mainly because he completely removes many of our grounded tools entirely, while still having ways to check air control. Considering Olimar's an even better camp character, I can definitely see him being even harder to deal with than Megaman in some ways-- though, while Olimar is probably harder to approach than Megaman, I feel like MM may control ground space a bit more aggressively? Almost zero experience playing against either though, barring AI and one or two randoms online, though, so much of that's theorycrafting.
Other than that... I'd have to say the times I played Inkling mirrors were the most painful MU, by far. Between not being able to tell who is who and both being so damned nimble, I'm getting lost in a 1v1 as if it were 8 player smash with items on in new pork city, jegus.
