To an extent, they feel this way about lifelines (though they do work out in some races—the second Super Mario Sunshine race comes to mind). This is especially the case with Pokémon FireRed, where they agreed the lifelines were a poorly handled idea that prolonged the Versus to an unnecessary degree.
They're not fond of their earlier habit of asking each other about their current gameplay progress, since they feel it disrupted the flow of commentary and wasn't entertaining for the viewers. And even though they got some laughs by lying about their progress during Ocarina of Time, they found this annoying in hindsight and agreed to stop it. With Twilight Princess, they even changed their recording setup to allow them to see each other's live gameplay footage, putting this issue to rest.
Creator's Apathy: Josh admitted during Donkey Kong Country Versus that he doesn't properly edit his videos, but just skims through them and edits solely based on the wavelengths. This is evident in Pokémon FireRed Versus, where he never edits in anything asked of him (like pictures or word game scores), onscreen stats can be inconsistent, and Tyler's mic volume constantly fluctuates rather than Josh adjusting it.
When Josh started livestreaming Super Mario Sunshine speedruns in 2016, this pretty much crushed anyone's hopes and theories that they'd do a third Versus of the game; even if it did happen, it'd be horribly one-sided.
When Tyler pretty much stopped doing videos on his own channel, and mentioned in some stories he told that he was no longer interested in making videos and instead studying to become a civil engineer, people thought this meant he'd be departing from Versus soon. However, he's refuted this and plans to remain loyal to Versus, though he and Josh often joke about replacing him (not that this is new). Further jossed when Tyler started making videos again and seemingly went back on what he said previously, saying he loves making them * It's possible that when he said he was no longer interested in making videos, he meant making them as a career and still enjoys them as a hobby.
Schedule Slip: They have experienced several. It's a Running Gag for them to announce an update schedule (usually for a new series or after a hiatus), then only stick to it for one or two weeks before falling back on "whenever it's done". They do have busy lives, so it's understandable, but most fans at least wish they'd just stop promising schedules they can't stick to.