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Well, I am not very happy either about the renaming of quite common pieces
in Superchess. But when in Rome, one does like the Romans...

The use of the [] came more or less automatic, as I started defining
Superchess in WinBoard as a form of Crazyhouse. I am not entirely happy
with that either, as the 'holdings' here have a different meaning than
in Crazyhouse (promotion pieces in stead of drop pieces).

OTOH, and this we discussed before, I am skeptical about your desire to be
able to encode the rules of the game in the FEN. Even requiring that each
piece has a unique letter, which is universally valid over all variants,
is doomed: as John remarked below, there are more pieces than letters. So
whatever system you devised, it would necessarily be limited to a subset
of the variants. While other variants would still need FENs.

For the sub-variant of Superchess played at the Dutch Championship, it
would be feasible to unify it with Capablanca-type variants.

If you want a FEN format which uniquely specifies the variant, which is
usable over a wide range of variants, I think you should build in a way to
specify exotic pieces (for which no standard letter exists). What I would
do is to allow replacement of a single piece letter by a description of
the piece in parentheses. E.g. in stead of G for Giant/Amazon you could
use (QN). 

So you would get FENs like:

3k4/6(QN)1/8/8/8/8/8/3KN w - - 0 1

Then you would only need a fairly limited set of move-descriptor
letters for use within the parentheses. You could use B,R,Q to indicate
sliders (where Q would be shorthand for RB), and the Betza system ( http://www.chessvariants.org/piececlopedia.dir/betzanot.html ) built on F, W, A, D, N, H, L, J, G for leapers. Repetition of a leaper symbol would indicate a slider with that step (i.e. (NN) would be Nightrider, B would be shorthand for (FF)).

For compactness, you could allow definition of shorthand letters within
the FEN: (NN=H) would mean that subsequent H or h (without parentheses)
would indicate white and black Nightriders, respectively. This would be
especially important for Pawns, of which there usually are a lot. And
promotion rules are a property of a Pawn, so Pawns with non-standard
promotion rules would need to be described. A Pawn that could promote only
to Ferz (like in Shatranj) could be designated as (P:F). I would use an
explicit negation character for excluding pieces, like (P:!C) in Janus.
And of course define a shorthand letter for it, as there are likely to be
many Pawns in most Janus positions, (P:!C=P), so all subsequent Pawns
would be simply P or p. (P:*) could mean promotable to every captured
piece. Superchess positions would allow promotion to some pieces that were
replaced in the prelude as well as to captured pieces, which could be
written as (P:*qbbn=P), where lower-case indicates the piece is in finite
supply.