diff --git a/IPython/config/application.py b/IPython/config/application.py
index 3723fff..90607ee 100644
--- a/IPython/config/application.py
+++ b/IPython/config/application.py
@@ -24,6 +24,7 @@ import os
 import re
 import sys
 from copy import deepcopy
+from collections import defaultdict
 
 from IPython.config.configurable import SingletonConfigurable
 from IPython.config.loader import (
@@ -329,6 +330,51 @@ class Application(SingletonConfigurable):
         self.subapp = subapp.instance()
         # and initialize subapp
         self.subapp.initialize(argv)
+    
+    def flatten_flags(self):
+        """flatten flags and aliases, so cl-args override as expected.
+        
+        This prevents issues such as an alias pointing to InteractiveShell,
+        but a config file setting the same trait in TerminalInteraciveShell
+        getting inappropriate priority over the command-line arg.
+
+        Only aliases with exactly one descendent in the class list
+        will be promoted.
+        
+        """
+        # build a tree of classes in our list that inherit from a particular
+        # it will be a dict by parent classname of classes in our list
+        # that are descendents
+        mro_tree = defaultdict(list)
+        for cls in self.classes:
+            clsname = cls.__name__
+            for parent in cls.mro()[1:-3]:
+                # exclude cls itself and Configurable,HasTraits,object
+                mro_tree[parent.__name__].append(clsname)
+        # flatten aliases, which have the form:
+        # { 'alias' : 'Class.trait' }
+        aliases = {}
+        for alias, cls_trait in self.aliases.iteritems():
+            cls,trait = cls_trait.split('.',1)
+            children = mro_tree[cls]
+            if len(children) == 1:
+                # exactly one descendent, promote alias
+                cls = children[0]
+            aliases[alias] = '.'.join([cls,trait])
+        
+        # flatten flags, which are of the form:
+        # { 'key' : ({'Cls' : {'trait' : value}}, 'help')}
+        flags = {}
+        for key, (flagdict, help) in self.flags.iteritems():
+            newflag = {}
+            for cls, subdict in flagdict.iteritems():
+                children = mro_tree[cls]
+                # exactly one descendent, promote flag section
+                if len(children) == 1:
+                    cls = children[0]
+                newflag[cls] = subdict
+            flags[key] = (newflag, help)
+        return flags, aliases
 
     def parse_command_line(self, argv=None):
         """Parse the command line arguments."""
@@ -350,9 +396,12 @@ class Application(SingletonConfigurable):
         if '--version' in argv:
             self.print_version()
             self.exit(0)
+        
+        # flatten flags&aliases, so cl-args get appropriate priority:
+        flags,aliases = self.flatten_flags()
 
-        loader = KVArgParseConfigLoader(argv=argv, aliases=self.aliases,
-                                        flags=self.flags)
+        loader = KVArgParseConfigLoader(argv=argv, aliases=aliases,
+                                        flags=flags)
         try:
             config = loader.load_config()
             self.update_config(config)
diff --git a/IPython/config/tests/test_application.py b/IPython/config/tests/test_application.py
index 0e69cab..94588cc 100644
--- a/IPython/config/tests/test_application.py
+++ b/IPython/config/tests/test_application.py
@@ -17,9 +17,11 @@ Authors:
 # Imports
 #-----------------------------------------------------------------------------
 
+import logging
 from unittest import TestCase
 
 from IPython.config.configurable import Configurable
+from IPython.config.loader import Config
 
 from IPython.config.application import (
     Application
@@ -60,11 +62,14 @@ class MyApp(Application):
                     'j' : 'Foo.j',
                     'name' : 'Foo.name',
                     'enabled' : 'Bar.enabled',
-                    'log-level' : 'MyApp.log_level',
+                    'log-level' : 'Application.log_level',
                 })
     
     flags = Dict(dict(enable=({'Bar': {'enabled' : True}}, "Set Bar.enabled to True"),
-                  disable=({'Bar': {'enabled' : False}}, "Set Bar.enabled to False")))
+                  disable=({'Bar': {'enabled' : False}}, "Set Bar.enabled to False"),
+                  crit=({'Application' : {'log_level' : logging.CRITICAL}},
+                        "set level=CRITICAL"),
+            ))
     
     def init_foo(self):
         self.foo = Foo(config=self.config)
@@ -129,6 +134,30 @@ class TestApplication(TestCase):
         self.assertEquals(app.bar.enabled, True)
         self.assertEquals(app.bar.b, 10)
     
+    def test_flatten_flags(self):
+        cfg = Config()
+        cfg.MyApp.log_level = logging.WARN
+        app = MyApp()
+        app.update_config(cfg)
+        self.assertEquals(app.log_level, logging.WARN)
+        self.assertEquals(app.config.MyApp.log_level, logging.WARN)
+        app.initialize(["--crit"])
+        self.assertEquals(app.log_level, logging.CRITICAL)
+        # this would be app.config.Application.log_level if it failed:
+        self.assertEquals(app.config.MyApp.log_level, logging.CRITICAL)
+    
+    def test_flatten_aliases(self):
+        cfg = Config()
+        cfg.MyApp.log_level = logging.WARN
+        app = MyApp()
+        app.update_config(cfg)
+        self.assertEquals(app.log_level, logging.WARN)
+        self.assertEquals(app.config.MyApp.log_level, logging.WARN)
+        app.initialize(["--log-level", "CRITICAL"])
+        self.assertEquals(app.log_level, logging.CRITICAL)
+        # this would be app.config.Application.log_level if it failed:
+        self.assertEquals(app.config.MyApp.log_level, "CRITICAL")
+    
     def test_extra_args(self):
         app = MyApp()
         app.parse_command_line(["--Bar.b=5", 'extra', "--disable", 'args'])
diff --git a/IPython/parallel/apps/ipclusterapp.py b/IPython/parallel/apps/ipclusterapp.py
index 0d77895..adf8222 100755
--- a/IPython/parallel/apps/ipclusterapp.py
+++ b/IPython/parallel/apps/ipclusterapp.py
@@ -374,12 +374,6 @@ start_aliases.update(dict(
 ))
 start_aliases['clean-logs'] = 'IPClusterStart.clean_logs'
 
-# set inherited Start keys directly, to ensure command-line args get higher priority
-# than config file options.
-for key,value in start_aliases.items():
-    if value.startswith('IPClusterEngines'):
-        start_aliases[key] = value.replace('IPClusterEngines', 'IPClusterStart')
-
 class IPClusterStart(IPClusterEngines):
 
     name = u'ipcluster'