Now, assuming that this would let us have a bit of control over the canon...
I think the first movie would have been great if we had a bit at the beginning showing us the Toa Mata's arrival, the Rahi, Bohrok and transformation. You know, as a 10 to 20-minute prologue to set everything up. Also, tone up the fight scenes a little bit and maybe add a couple of infected matoran. The ending would also be more serious and we would actually see the Turaga lead everyone into Metru Nui instead of three of them standing and casting a beam of light. Also, Matau and Whenua would get more lines, I don't think they spoke a word. At least Onewa had 2 lines in the thing so his model was worth it. That and Matoran in the background should also wear mata masks and not just nobles.
For the second, I think we could have done with a proper introduction to Lhikahn and better establishment of his link to Nidhiki. The line "you lost the right to call me Brother long ago" really didn't tell me much about their relationship. Also, for the longest time I thought nidhiki was a girl. He just sounds like a woman putting on a raspy voice after smoking. When I first saw LOMN i thought Lhikan was Jaller and went "what the Kane-Ra? When did Jaller become a Toa?!". Also, I think the search for the Great Disks should have been fleshed out a little and they could have been given reason to their lack of elemental power usage. Also, I'm still confused about that scene where Dume is talking to Makuta. I mean Dume would never have gone along with the plan so wasn't he in a pod at this time? How can Makuta be two beings at once, or was he just talking to himself? Gah.
Oh, and the 6 fake prophecised matoran would also play a role, and we'd see the big fight that happens on the way to Metru Nui. And I'd drop the Matau/Nokama relationship thing. Also, Nuju makes a vow at the end to only speak in riddles and gestures.
For Web of Shadows, I wouldn't touch too much. It seemed fine on its own. But perhaps a bit more of the Rhotuka usage and a little more backstory on the Rahaga would have been good. I mean they didn't really say much other than "I'm a Rahaga, and these are my fellows". Also in my version Keetongu doesn't kill Sidorak, but rather the Visorak seemingly devour him Lion King-style. A little extra information being given about Roodaka which doesn't require browsing through the DVD extras would be a nice touch as well.
Ideally, for TLR, I'd stop it existing entirely. But if I had to, I'd make sure it be made by not-tinseltown. I would probably start the film with the establishment of what happened during the Voya/Mahri Nui and Karda Nui arcs (particularly showcasing finding the Mask of Life, maybe show Velika for foreshadowing, Matoro's Death and the Toa Mata re-awakening the GSR. Then we see a movie version of everyone rejoicing in Metru Nui when Makuta reveals he's taken over. Cue Mask of Life with Mata Nui being thrown into space and landing on SM. The Iron Tribe gets more coverage, the Glatorians get trained to use their new powers, Mata Nui's fight against Tuma almost ends in a loss and transforms Tuma as a result, then they put together the giant robot and part two is about the massive fight and we get to see Tahu pwning rahkshi.
On a sub-not, TLR would also have its soundtrack replaced with the beautiful original trilogy's.