I seem to remember the only time a gundam was ever even beaten by a regular MS during the series was by Zechs in the tallgeese, and I'm pretty sure Heero was already wounded before the battle. The aforementioned vayeate and mercurius barely even count for giving the gundams a hard time because they A) Were made from gundanium, by an ex-project meteor scientist, B) They both had AIs based directly on gundam pilot main characters, and C) They end up getting blown up within an episode or two anyway. Include the non-project meteor Epyon into this list, and... Well, yeah. You can't really disprove that the main character's gundams weren't just character shielding it up until Endless Waltz.
EW itself... might have counted as a gundam loss if they didn't do the whole "Try to win without killing anyone!" thing. The MS serpents were supposed to be Oz's fanciest gundam-killing units from the end of the war in the first place. Did they actually knock out a single MS with a character inside? Even Noin's outdated Tarus? Nope. The Wing Zero more or less blew it's own arms off, so I have no idea if that one counts or not.
It's not the worst anime space opera series by a long shot at any rate, but, I'm sorry, the technology and tactics were sillyville.
Legend of the Galactic Heroes is from the same-ish time period and has melodrama by the buckets, but still stands head and shoulders over GW because of the numerous unwinnable scenarios provided by it's attention to detail. That's the difference in my eyes, at least.