I thought the movie was excellent. The ending itself was perfect. If you keep in mind that the whole story arc of Fullmetal Alchemist is about two children that commit an awful sin and have to live with the consequences of it, I think the ending is satisfying.
Throughout the whole storyline, Equivalent Exchange is maintained:
1. Ed & Al commit a terrible sin. As payment, Al dies and Ed loses an arm.
2. Ed brings Al back to life. As payment, Ed loses his leg and Al is trapped in a metal suit of armor.
...skip ahead to end of series...
3. Al brings a murdered Ed back to life and gives him his real arm & leg. As payment, Al (and the rest of the Philosopher's Stone) is consumed.
4. Ed brings Al back to life in his full body. As payment, Ed is taken beyond the gate, he's stuck with his automail again and Al loses his memory.
...skip to movie...
5. Al opens the gate. As payment Wrath and the rest of the Philosopher's Stone (which I assume is what makes Gluttony superpowerful) is consumed.
6. Ed is reunited with Al. As payment a few (hundred) people decide to tag along and wreak havoc on Hagaren World.
7. Ed goes back through the gate to destroy the portal. However, he's finally reunited with his brother and Al has his memories back. As payment they're stuck in our crappy world.
However, they're together and have (most of) their bodies back. They can continue their journey and they have each other. Al can feel human again and they've fulfilled their goal.
Our lives are all about the choices we make and the mistakes that screw them up. They're also about learning from consequences and trying to fix those mistakes.
Bottom line: Equivalent Exchange isn't just about alchemy. It's about how everything you do has a consequence, a price you have to pay. Fullmetal Alchemist is about the Elrics learning that fact and dealing with it. Yeah, things are not the same since they commited the ultimate sin in alchemy and they shouldn't be. However, they have found a balance they can live with. Al has his body and Ed can live with his automail. They're together and the world is wide open for them to explore.
Other random thoughts:
The entrance of Mustang was really really cool. In fact all the battle scenes were very cool. I kinda expected Mustang to casually waltz in there like that and lay the smack down. I was not dissappointed.
I don't think I've ever seen a character look so fearsome while at the same time being totally goofy and silly. The Armstrong stone head alchemy thing was great. I fell out of my chair laughing.