Not in order of importance:
1) CONCAT will not properly handle REF arguments that are either REF(variable) that in itself is a REF to another variable or is of the form REF(a;b).
2) REF, CONCAT etc. will not work outside of numoccurs and value tags
3) USEREF does not work
4) EVAL should be more robust
5) EVAL should eventually migrate to a Java math parser like JEPLite (http://jeplite.sourceforge.net/) or JMEP (http://jmep.tigris.org/)
6) Constraints are not implemented
7) Aliases are not implemented and would help clean things up
8) 2D arrays should better show as 2D
9) Easy way to fill in values in an array
10) Easy way to reread a description or a whole set of descriptions
11) A way to reference the k-th element of an array is missing from LCML
12) A way to set all use/hidden to true/false/flip
13) Make sure that export/import works as advertized even if the description file is updated.
14) Extend LCML to have a use and a hide element at the set and at the description level in order to avoid having to use the "Dummy Variable" trick.
15) There should be a usable hide element for structures.