They should do a One Year War trilogy, and find ways to include parts or hints from all the OYW era stories (08thMS, 0080, etc.) into the main MSG timeline. Then, at the end of the 3rd in the trilogy, after the war is over, talk about how the next few years were spent sweeping up any zeon remnants and have a few 0083 scenes. That way, that whole section of the timeline is out of the way and they can jump right into Zeta if they choose to.
I think past Z Gundam though (and maybe ZZ...possibly Char's Counter Attack...) it would be better to start crafting new stories for live action films as opposed to simply translating every anime onto the screen. The new stories should in no way overlap the existing anime timeline, but exist in parallel, as events yet unexplored during the Gundam history. It gives the films an opprotunity to still be new and exciting to everyone and add in a positive way to the stories, without having everyone necessarily already know where it's going because the saw the anime version. I would do the whole Z, ZZ, CCA section of the timeline as a one movie each trilogy, and even then, I'd throw some different angles and perspectives into it just to change it up. Past that, once you get into the F91/V era, I would make up all new stories. Maybe draw from the manga, like crossbone or something, but it shopuld definitely be new or something that hasn't been animated. I'm just not really a fan of translating every Gundam anime to live action directly. The OYW is the only story I could see it being done that way. It has to, because it sets off the entire Gundam Saga.
As far as Transformers, the comparisons should stop at both films having robots that are bigger than humans. Gundam should be an intelligent science fiction action film. A tone similar to the newest Star Trek film. The mobile suits are simply weapons of war, and while the visuals may be unique and eye catching, they should no more take center stage than a nifty tank in a WW2 film. It is first and foremost a human drama. Of course the fight scenes should be appropriately mind blowing...
I actually have written a few Gundam stories and started on a Mobile Suit Gundam OYW script not too long ago. It's been somewhat of a dream of mine to be the one to adapt the Saga as a film.