Lack of an ending
I think the main complaint with EDF: IA is that it lacks a real ending. As it stands, the 15 missions feel like the first act of a larger story. I mean think about it, at the end of the 15th mission you haven't managed to liberate any cities from the ravagers. In fact you haven't even managed to save just one city (New Detroit)!
The other EDF/GDF games all ended with you personally gunning down the mothership, as unbelievable that would seem...though since when have these games been about believability?
There were also more units to face off against in the other games as well and they were more evenly spaced. I mean, come on, anthills and a small Hector in the first mission? Gunships in the second?