Layton's mystery journey is still very much a part of the Layton series, I don't see why the fact that the series having a new main protagonist would somehow invalidate Layton in any way, especially since he's still being promoted front and center right next to his daughter to this day. Their practically costars more than anything.
And the reason why Lady Layton didn't receive much fanfare was because the game itself is a very controversial entry within the Layton fanbase. Its more or less the black sheep of the Layton franchise. In fact there has been more demand for a new Layton game to the point that fans themselves have taken it upon them to develop a whole fangame themselves. There is definitely still a lot of interest in seeing the franchise return.
But it undeniably does complicate the situation when a series pivots to a new character, even as the daughter of Professor Layton proper, at least for people who are less aware of the titles or have fallen off after years and just see a new Layton game advertised through Lady Layton as opposed to the Professor Layton they may have once known. That sort of decision does tend to effect perception of your series and its characters.
And that's kind of my point. Lady Layton came and went without fanfare and stands as the most recent game in the series after most people would agree that Layton got a bit saturated quite quickly in the DS era. Much like Yokai Watch, Level 5 tripled down on a successful IP until the luster wore off and people just became less interested (I knew several people who just got behind on the Layton games and just stopped caring because they were coming out so frequently). I don't think Level 5 has really done much to rehabilitate that image, and Lady Layton being controversial like you said further contributes to Layton as a whole just being less of a presence in people's minds. A black sheep as the most recent release combined with how pretty much mishandled the series was in terms of its sudden rise to success means it falls further and further out of favor in the public consciousness. I mean seriously, the first 4 Layton games were released in a 2 year period, and then you had Layton go without a release for 4 years to land on Lady Layton after Arazan Legacy. That sort of situation will hurt any franchise with over-exposure followed by sudden lack of exposure.
Meanwhile, compare that to Ace Attorney, which regularly has crossover appearances in other titles (Thanks in large part due to how Capcom operates), gets his games re-released with a fair amount of fanfare every couple of years, and hasn't really seen the same dropoff that I know Layton experienced at any point. It's just been an overall more consistent IP that Capcom has managed better than Level 5 has managed Layton. And just genuinely, I see more of the Smash fan base rallying around Phoenix Wright than I do around Layton at this point.
I think Layton has a chance and certainly still has fans as you pointed out, but I'm just trying to explain why Layton seems so much less favored in speculation these days (and honestly both of them have suffered from the whole, "Wait, we can get
which third party characters now?" thing that makes people less inclined to support the "more traditionally Nintendo third parties").