Obvious nitpick: unnecessary replicator plot.
It was a good idea about turning one enemy against another by having the replicator infest the Ori ship, but they let it almost eat up the Odyssey from within. Also the many times it got hit by those ori beams - I wonder how much of the ZPM was depleted? It seems the shield is much stronger in the movie compared to the finale.
The replicator infested Mereck was creepy and especially when the repli-skelton was about to strike.
One thing about the replicator thing is that you know there will be some serious use of gun fire, that's the one big plus about it.
Final nitpick is that I don't like how there is a back and forth thing like every 1-4 min we see the Odyssey and another we see daniel and the others on the planet. I would like it if they had 8-9min on one group then moving to the others. Just my opinion. Also I 'kept a record' over how long the replicator-Odyssey segment took and it was about 16-17min of the Sci-Fi aired version.
I was disappointed they didn't show anything new about Universe that I had already seen during the BSG finale. And it's not fair that BSG's 2nd airing of the finale gets to run like 2 hours 8-11min while they cut Ark of Truth to fit 2 hours rather than to show the whole movie and let it over run like 7-10 min. I think ZZbeach would agree.