In the lisp universe the future was in the 80's, thats when we tried the whole "structural editors" idea and concluded that they didn't work out as nicely as we hoped. I believe the sgml people tried them too, with poor results as well.
Paredit, a favorite among modern Lisp users, was directly inspired by Interlisp's structure editing. Paredit's own author calls it a "cheesy imitation" of Interlisp. (http://mumble.net/~campbell/emacs/paredit.credits)
Personally, I think Lisp is ripe for many different visual/kinesthetic interpretations, and this one certainly is pretty.
Personally I think structured editing is an idea that seems great until you actually try it.
(When I last observed someone editing Common Lisp code without turning on Paredit, it was rather depressing, how much time he spent closing parens and re-indenting everything. But maybe you use something else which avoids this problem?)
Reader macros (in the worst-case scenario you describe) are a very rare use-case, and therefore probably not worth optimizing an IDE for. Perhaps for you they're common, but I'm virtually certain that most Common Lisp users have never written even one. If macros are already uncommon to write, reader macros have a far higher bar of justification.
Two things that save time when indenting code and work in all Emacs programming modes:
1. (global-set-key (kbd "RET") 'newline-and-indent) in .emacs to automatically indent every newline (also points out problems in your syntax right away)
2. C-Space to start region selection, C-M-b or C-M-f to jump back/forward a code block (s-exp), then C-M-\ to reindent region.
The other thing I use is my https://github.com/vsedach/mouse-copy mode for "structured" copy and paste. It's convenient sometimes.
I use reader macros a lot more than Common Lisp programmers do now, and I encourage people to use them and think that reader macro usage will become more widespread, in particular due to Tobias Rittweiler's named-readtables library (http://common-lisp.net/project/named-readtables/).
In particular, I use cl-interpol (http://weitz.de/cl-interpol/) both for string interpolation and to do HTML templating (http://paste.lisp.org/display/118522). I also wrote a uri-temple library for Common Lisp (http://common-lisp.net/project/uri-template/). When I used CL-SQL, I used its reader macro syntax, and I thought it was worthwhile, but could have been better designed.
As for your last sentence, Erik Naggum who had a bad opinion on structure editors in general, seems to have liked the idea of a structure inspector, as in using such tools to inspect code, ratter than create it: http://www.xach.com/naggum/articles/3064225496493947@naggum....
There's a lot of usability failure in Lisp's history but I know that a great structure editor is possible.