This is a list of features, that would be nice to have:

Decompiler:
 - deinline inlined methods.
 - remove string decrypt method.
 - remove synthetic methods if and only if all calls to them are resolved.
 ~ handle try catch more thouroughly/safely.
 ~ decompile jode.jvm.Interpreter (hand optimized bytecode)

Obfuscator:
 - read options from a script.
 - flow obfuscation/optimization.
 - warn about Class.forName and list occurences.

DeObfuscator:
 - generate nice names:
    - classes: derive name from super. 
    - fields:  derive name from type.
 - give synthetic methods the right attribute and name (e.g. class$)
 - detect inner classes and give suitable names.
 
User Interface:
 - make a nice user interface:
   ~ list classnames: toggable between class hierarchie/package hierarchie.
   - list fields/method of selected class.
   - show decompilation of selected method.
   - show usage of method/fields.
 - syntax highlighting, hyper links etc.  (look at java.swing.JEditorPane)
 - visual obfuscation/deobfuscation (like klassmaster?, better?)

Internal:
 - clean up package hierarchy, esp. expr, flow and decompiler.