Current Google App Engine architecture lead to major problem with 200 index 
limitation since:

   1. Queries requires many indexes sometimes little overlapping - for 
   example I have (A, B, C) with sort on (D) but it is required to create also 
   (A, B) for sort on (D) - try to add some algorithm reducing number of 
   required indexes especially overlapping.
   2. Good practice it to create many models to separate code - it leads to 
   some index duplication - for example I want have different types of time 
   reservation in different tables not merge all types into one table to 
   complicate development - do not force users to write bad and complex code.
   3. Medium or large application need operate on 100-200 tables or more - 
   if tables will require composite indexes it mean that is not possible to 
   develop some kind of application on Google App Engine.

I think that better to charge us for service (indexes i/o) than limit 
development to small or medium application which not use too much indexing.

http://code.google.com/p/googleappengine/issues/detail?id=8305&sort=-id&colspec=ID%20Type%20Component%20Status%20Stars%20Summary%20Language%20Priority%20Owner%20Log

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