Here is a list of similarities:
1. The characters. Although Shinji and Sousuke, are, obviously, quite different, their situations are somewhat similar and many supporting characters, such as Asuka and Chidori, Misato and Mao, Kurz and Kaji, Shinji (the FMP one) and the NGE military nerd, are remarkably similar and it is hard not to believe that NGE influenced the FMP creators greatly.
2. Military complexes with huge amounts of funding to run mechas. Not much to say here.
3. The "light plot-to-serious plot" phenomenon is present in both series. In FMP, it starts out with Mithirl kicking ass for the first 24 episodes and then going on to Sousuke's and Chidori's personal issues and Mithril almost getting it's own ass kicked before kicking ass.
In NGE, it starts out with Angel after Angel getting pwned, as each one gets harder to kill the characters sink into their psyches and the whole ordeal becomes a surreal mindtrip full of Judeo-Christian undertones, which finally ends as a huge battle where NERV loses and Shinji figures out what he's worth or something really complicated like that and saves the world from collectivism.
Also, with the FMP novels going farther and farther down the plot device of the Whispered, it seems to be turning out like NGE.
4. Pilot/Mecha interface and the Lambda Driver and AT Field. Again, not much to say about an energy field/weapon used by mechas and powered by the pilot's concentration. Also: the Evas are living creatures that synchronize with their pilots and the FMP mechs having AIs that do something similar (ARX-7).
5. The FMP control room and the NERV control room. In one episode in TSR, there was a control room that looked almost exactly like the NGE one with the lights turned off.
6. Is that it? I can't think of much else at the moment.
So basically, FMP is heavily ripped off of NGE. However it is still awesome, and in some respects much better than NGE.
______________________
Now, while watching TSR again with my cousin (who I have successfully brainwashed into thinking that FMP is great

You know the whore in Hong Kong who looked exactly like Kaname except more sleazy? She was Kaname, but in disguise, perhaps bolstered by her success in Fumofu that we saw earlier. And, in order to strengthen the act, she even learned some Cantonese phrases. Her being Chidori explains why she speaks perfect Japanese, acts similar, and got mad when Sousuke failed to do her. After her initial plan to get laid failed, she went to Plan B to confront sousuke directly and "leap into his arms." This, too, had limited success.
Ah... Interpretations, interpretations.
Anybody agree with my proposals? It's okay if you don't, I was just throwing out my observations and the second one wasn't even serious.