So Emory to me is in an interesting class of “best private research university in a major non-Northeastern/Chicago city”, along with Georgetown, Rice, WUSTL, and USC. For a variety of reasons the “top” privates have not played quite the same role in elite family circles in these regions as they did in the Northeast or Chicago, and that is typically reflected in things like their application volumes (and hence admissions rates) and peer reputation surveys and so on.
Nonetheless I think from a branding perspective there is a plausible competitive advantage in being the “top” such university in a major city. Like you asked if Emory is “regarded as lesser, especially up north?” Well, lesser than what? Reputationally, it would be fair to say it is probably not seen as quite a peer of institutions like Harvard or MIT (the “top” such universities in Boston), Yale or Columbia (New York’s), Penn (Philly), Hopkins (Baltimore), or Chicago and Northwestern (Chicago). But around two seems the limit even for the biggest cities, so I would not personally be concerned about Emory being seen as “lesser” than like NYU or Boston College, if anything more the opposite.
Of course what really dominates placement in next steps after these colleges is how you do as an individual. But to the extent it matters at all, I think if anything there might be an advantage at looking at next steps in the Northeast and yet coming from one of these very well-regarded “top in a non-Northeastern city” universities, versus being one of the hordes from not-quite-top-in-their-market privates in the Northeast.
In terms of culture, similar to, say, USC, Emory long might have been seen as somewhat toward the less academicky side in this group. But I think a lot of that is changing (for USC too) as this class of universities is just getting systematically more selective. At this point, I think people understand Emory is a “serious”/“rigorous” place academically, even if the culture is committed to being collaborative instead of competitive. Of course there are individual programs where Emory is considered more or less prominent as a research university, but for college purposes I would not really worry about the rigor of anything it actually offers.
OK, so does that sound good to you or not? That’s entirely up to you, but I think some people really enjoy getting out of the Northeast rat-race for college, and Emory and the other colleges I mentioned in this group are a really interesting opportunity to do that. But if you thrive on that sense of constant competition with your peers, maybe you would prefer just to go to the “best” Northeastern college that will admit you–certainly a popular approach, even if some of us don’t see it as particularly desirable in terms of college experience.