Movie maker vs After Effects
First of all you can't compare AE and Movie Maker. Secondly, what were the codec and bit rate settings in both programs?
If all settings were the same, then the one with the higher frame rate should normally produce a larger file size. However if one program was set to use a higher bit rate or a different codec that compresses less, then that one will produce a larger file size.
Additionally you should use Premiere for editing videos, After Effects is Adobe's motion graphics and special effects editor.
The problem you have with the quality of the video after editing is most likely due to the settings you used for export. A good codec should not reduce the quality too significantly, even if it compresses the file.
I would also recommend you try out Lightworks Free, DaVinci Resolve 12 Free or Hitfilms Express 3.
