I think Tomino is the main reason behind GG's demise. He won't let them republish any of the novels or radio drama CDs, and IIRC, when fans asked for him to give permission for the publisher to put GG back in production, he said something along the lines that he was crazy when he penned it and to forget about it like it never existed. So, even if going against the will of the fans, Tomino doesn't want it around anymore. Perhaps he doesn't like it, but he didn't like Victory Gundam either, but V has a big fanbase.
As far as reasons stated by people as whats in GG that contridicts areas of the timeline such as F-91 and V, they mostly state the technology, mainly that the MS(or "Man-Machines") are back to a size around like that of the 0090-0105era, and I believe IIRC that Beam Shield aren't used. Well, from what I know of Gaia Gear tech, those are the only things. Perhaps going big again in size is the thing to do to get the highest performance possible at the time. And with the wide used of I-Fields on the best suits of the era, perhaps with that no Beam Shield is needed, or it can't power both, so going with a traditional shield and having a I-Field is the best bet. And to refer on the situation of non-I-Fielders having regular shields, well, perhaps power requirements, or MS high-speed renders the Beam Shield unable to operate on this era of suits, or no longer needed. I suspect the metal shields of the era to be far superior to those used before wide use of Beam Shields, and I would think that the cost of these new and improved regular shields would still be far lower than a Beam Shield.
Overall, I think GG from what I've seen at least could still fit in the UC timeline. Perhaps if Tomino doesn't like it how it is, maybe he should remake it, at least in a revised novel series, to make it to his likeing, better, more canonicle or whatever.
Tomino maybe letting up on his boycott on the present form, however. I think they re-released the music soundtracks of the music from the radio dramas. However, that doesn't mean a re-release of other GG related goods is around the corner.