I agree with most of the general consensus that while the newer theatres are more comfortable, they are also the worst in terms of the architecture.
I had seen a lot of shows around 1998-2007 but have only started seeing more since moving here recently so a few theatres I haven't had the pleasure of revisiting and can only vaguely remember them (such as the Broadway and the Imperial).
I do think of the newer theatres, I agree The Lyric (nee Ford and Hilton and Foxwoods) is the one that has the most charm along with the comfort...and what a great lobby. Granted I am also a little biased since my first show was Ragtime so I have those fond memories.
Since the remolded the Miller and it became the Sondheim, I find while it isn't exactly "charming", it is definitely a very sleak theatre unlike the Marquis or Minskoff.
As for the beauty:
New Amsterdam
Belasco
Lyceum
and if only the Mark Hellinger were still a Broadway house. It is truly stunning.