I think Ike beats Marth pretty clearly this time around, actually. Ike wins in Neutral which is where the majority of matchups are decided in general. One of Ike's biggest problems in Brawl against Marth was dealing with Marth's pokes and pressure from a defensive position, especially out of shield. From shielding Ike didn't have too many solid responses to just about anything Marth could throw out in neutral and as we all know shielding was surpremely powerful and essential in Brawls gameplay.
Marth's pokes are nowhere near as scary as they used to be and trades are still awfully lopsided in Ike's favor. Unless Marth gets that birthday surprise gimp on Ike he'll be fighting an uphill battle. There's no way Marth wins this matchup now imo ... and that's not even taking Ike's custom specials into account.
I think you're really downplaying how important Marth's mobility and counter is. Ike also still actually doesn't have great OOS punishes for Marth's spaced aerials such as N-air and fullhop F-air. Only Ike's B-air has decent startup and range, but it also only really hits horizontally, and doesn't exactly have more range than most of Marth's stuff.
Marth does have to play carefully around Ike's autocanceled F-air and more damaging tilts which are all safe on block, but when you're as mobile as Marth, you have to realize that the difficulty of whiff punishing is sorta trivialized. If anything, both characters are likely to be forced to play super respectfully during neutral. Just Marth has an easier time getting away with moves that can't be reacted to in the air, while Ike's primary advantage is knowing that he has greater consistency in close range.
Marth doesn't have to work exceptionally hard to either gimp Ike or kill him. It's simply a matter of forcing Ike offstage. Both Ike's SideB and Up-B are very punishable by Marth, and in the few situations where Ike is close enough to the stage to recover without those moves, it's a pure guess not in his favor to defend against Marth's tipper aerial edgeguards. In the meantime, most of Ike's juggle trap options become a liability except perfectly spaced U-air to avoid Counter, but in general, Ike doesn't have a lot of good options for actually killing Marth when a lot of his best options for KOing out of juggles are much less effective in the presence of Counter.
Ike builds damage better than Marth, that I can probably agree on, but Marth actually still has many safe tools in this matchup that he used to have. And his KO options are very noticeably better and more reliable.
Custom Ike, I could buy that he beats Custom Marth with Windbox Eruption and Close Combat being generally amazing options that complete Ike's game. Default settings though, nerfs to Marth's aerials just mean Ike doesn't get crushed by Marth playing hyper aggressively, but doesn't change that he still has to put in noticeable work and commitment to get around Marth's superior mobility and air spacing options, and the fact he loses out on juggles and edgeguards very noticeably.